diff --git a/bundle/config/mutator/run_as_test.go b/bundle/config/mutator/run_as_test.go
index c57de847..67bf7bcc 100644
--- a/bundle/config/mutator/run_as_test.go
+++ b/bundle/config/mutator/run_as_test.go
@@ -18,7 +18,7 @@ import (
 
 func allResourceTypes(t *testing.T) []string {
 	// Compute supported resource types based on the `Resources{}` struct.
-	r := config.Resources{}
+	r := &config.Resources{}
 	rv, err := convert.FromTyped(r, dyn.NilValue)
 	require.NoError(t, err)
 	normalized, _ := convert.Normalize(r, rv, convert.IncludeMissingFields)
@@ -154,6 +154,11 @@ func TestRunAsErrorForUnsupportedResources(t *testing.T) {
 	v, err := convert.FromTyped(base, dyn.NilValue)
 	require.NoError(t, err)
 
+	// Define top level resources key in the bundle configuration.
+	// This is not part of the typed configuration, so we need to add it manually.
+	v, err = dyn.Set(v, "resources", dyn.V(map[string]dyn.Value{}))
+	require.NoError(t, err)
+
 	for _, rt := range allResourceTypes(t) {
 		// Skip allowed resources
 		if slices.Contains(allowList, rt) {
diff --git a/bundle/deploy/terraform/convert_test.go b/bundle/deploy/terraform/convert_test.go
index e1f73be2..7ea44853 100644
--- a/bundle/deploy/terraform/convert_test.go
+++ b/bundle/deploy/terraform/convert_test.go
@@ -455,6 +455,24 @@ func TestBundleToTerraformModelServingPermissions(t *testing.T) {
 	var src = resources.ModelServingEndpoint{
 		CreateServingEndpoint: &serving.CreateServingEndpoint{
 			Name: "name",
+
+			// Need to specify this to satisfy the equivalence test:
+			// The previous method of generation includes the "create" field
+			// because it is required (not marked as `omitempty`).
+			// The previous method used [json.Marshal] from the standard library
+			// and as such observed the `omitempty` tag.
+			// The new method leverages [dyn.Value] where any field that is not
+			// explicitly set is not part of the value.
+			Config: serving.EndpointCoreConfigInput{
+				ServedModels: []serving.ServedModelInput{
+					{
+						ModelName:          "model_name",
+						ModelVersion:       "1",
+						ScaleToZeroEnabled: true,
+						WorkloadSize:       "Small",
+					},
+				},
+			},
 		},
 		Permissions: []resources.Permission{
 			{
diff --git a/bundle/permissions/filter.go b/bundle/permissions/filter.go
index 6d39630c..60264f6e 100644
--- a/bundle/permissions/filter.go
+++ b/bundle/permissions/filter.go
@@ -66,6 +66,11 @@ func (m *filterCurrentUser) Apply(ctx context.Context, b *bundle.Bundle) diag.Di
 	err := b.Config.Mutate(func(v dyn.Value) (dyn.Value, error) {
 		rv, err := dyn.Get(v, "resources")
 		if err != nil {
+			// If the resources key is not found, we can skip this mutator.
+			if dyn.IsNoSuchKeyError(err) {
+				return v, nil
+			}
+
 			return dyn.InvalidValue, err
 		}
 
diff --git a/libs/dyn/convert/from_typed.go b/libs/dyn/convert/from_typed.go
index e5fb0de6..af49a07a 100644
--- a/libs/dyn/convert/from_typed.go
+++ b/libs/dyn/convert/from_typed.go
@@ -12,26 +12,24 @@ import (
 type fromTypedOptions int
 
 const (
-	// If this flag is set, zero values for scalars (strings, bools, ints, floats)
-	// would resolve to corresponding zero values in the dynamic representation.
-	// Otherwise, zero values for scalars resolve to dyn.NilValue.
+	// If this flag is set, zero values in the typed representation are resolved to
+	// the equivalent zero value in the dynamic representation.
+	// If it is not set, zero values resolve to [dyn.NilValue].
 	//
-	// This flag exists to reconcile the default values for scalars in a Go struct
-	// being zero values with zero values in a dynamic representation. In a Go struct,
-	// zero values are the same as the values not being set at all. This is not the case
-	// in the dynamic representation.
-	//
-	// If a scalar value in a typed Go struct is zero, in the dynamic representation
-	// we would set it to dyn.NilValue, i.e. equivalent to the value not being set at all.
-	//
-	// If a scalar value in a Go map, slice or pointer is set to zero, we will set it
-	// to the zero value in the dynamic representation, and not dyn.NilValue. This is
-	// equivalent to the value being intentionally set to zero.
-	includeZeroValuedScalars fromTypedOptions = 1 << iota
+	// This flag exists to reconcile default values in Go being zero values with values
+	// being intentionally set to their zero value. We capture zero values in the dynamic
+	// configuration if they are 1) behind a pointer, 2) a map value, 3) a slice element,
+	// in the typed configuration.
+	includeZeroValues fromTypedOptions = 1 << iota
 )
 
 // FromTyped converts changes made in the typed structure w.r.t. the configuration value
 // back to the configuration value, retaining existing location information where possible.
+//
+// It uses the reference value both for location information and to determine if the typed
+// value was changed or not. For example, if a struct-by-value field is nil in the reference
+// it will be zero-valued in the typed configuration. If it remains zero-valued, this
+// this function will still emit a nil value in the dynamic representation.
 func FromTyped(src any, ref dyn.Value) (dyn.Value, error) {
 	return fromTyped(src, ref)
 }
@@ -48,18 +46,18 @@ func fromTyped(src any, ref dyn.Value, options ...fromTypedOptions) (dyn.Value,
 		}
 		srcv = srcv.Elem()
 
-		// If a pointer to a scalar type points to a zero value, we should include
+		// If a pointer to a type points to a zero value, we should include
 		// that zero value in the dynamic representation.
 		// This is because by default a pointer is nil in Go, and it not being nil
 		// indicates its value was intentionally set to zero.
-		if !slices.Contains(options, includeZeroValuedScalars) {
-			options = append(options, includeZeroValuedScalars)
+		if !slices.Contains(options, includeZeroValues) {
+			options = append(options, includeZeroValues)
 		}
 	}
 
 	switch srcv.Kind() {
 	case reflect.Struct:
-		return fromTypedStruct(srcv, ref)
+		return fromTypedStruct(srcv, ref, options...)
 	case reflect.Map:
 		return fromTypedMap(srcv, ref)
 	case reflect.Slice:
@@ -80,7 +78,7 @@ func fromTyped(src any, ref dyn.Value, options ...fromTypedOptions) (dyn.Value,
 	return dyn.InvalidValue, fmt.Errorf("unsupported type: %s", srcv.Kind())
 }
 
-func fromTypedStruct(src reflect.Value, ref dyn.Value) (dyn.Value, error) {
+func fromTypedStruct(src reflect.Value, ref dyn.Value, options ...fromTypedOptions) (dyn.Value, error) {
 	// Check that the reference value is compatible or nil.
 	switch ref.Kind() {
 	case dyn.KindMap, dyn.KindNil:
@@ -108,12 +106,22 @@ func fromTypedStruct(src reflect.Value, ref dyn.Value) (dyn.Value, error) {
 			return dyn.InvalidValue, err
 		}
 
-		if nv != dyn.NilValue {
+		// Either if the key was set in the reference or the field is not zero-valued, we include it.
+		if ok || nv != dyn.NilValue {
 			out.Set(refk, nv)
 		}
 	}
 
-	return dyn.NewValue(out, ref.Location()), nil
+	// Return the new mapping if:
+	// 1. The mapping has entries (i.e. the struct was not empty).
+	// 2. The reference is a map (i.e. the struct was and still is empty).
+	// 3. The "includeZeroValues" option is set (i.e. the struct is a non-nil pointer).
+	if out.Len() > 0 || ref.Kind() == dyn.KindMap || slices.Contains(options, includeZeroValues) {
+		return dyn.NewValue(out, ref.Location()), nil
+	}
+
+	// Otherwise, return nil.
+	return dyn.NilValue, nil
 }
 
 func fromTypedMap(src reflect.Value, ref dyn.Value) (dyn.Value, error) {
@@ -146,7 +154,7 @@ func fromTypedMap(src reflect.Value, ref dyn.Value) (dyn.Value, error) {
 		}
 
 		// Convert entry taking into account the reference value (may be equal to dyn.NilValue).
-		nv, err := fromTyped(v.Interface(), refv, includeZeroValuedScalars)
+		nv, err := fromTyped(v.Interface(), refv, includeZeroValues)
 		if err != nil {
 			return dyn.InvalidValue, err
 		}
@@ -183,7 +191,7 @@ func fromTypedSlice(src reflect.Value, ref dyn.Value) (dyn.Value, error) {
 		}
 
 		// Convert entry taking into account the reference value (may be equal to dyn.NilValue).
-		nv, err := fromTyped(v.Interface(), refv, includeZeroValuedScalars)
+		nv, err := fromTyped(v.Interface(), refv, includeZeroValues)
 		if err != nil {
 			return dyn.InvalidValue, err
 		}
@@ -206,7 +214,7 @@ func fromTypedString(src reflect.Value, ref dyn.Value, options ...fromTypedOptio
 	case dyn.KindNil:
 		// This field is not set in the reference. We set it to nil if it's zero
 		// valued in the typed representation and the includeZeroValues option is not set.
-		if src.IsZero() && !slices.Contains(options, includeZeroValuedScalars) {
+		if src.IsZero() && !slices.Contains(options, includeZeroValues) {
 			return dyn.NilValue, nil
 		}
 		return dyn.V(src.String()), nil
@@ -226,7 +234,7 @@ func fromTypedBool(src reflect.Value, ref dyn.Value, options ...fromTypedOptions
 	case dyn.KindNil:
 		// This field is not set in the reference. We set it to nil if it's zero
 		// valued in the typed representation and the includeZeroValues option is not set.
-		if src.IsZero() && !slices.Contains(options, includeZeroValuedScalars) {
+		if src.IsZero() && !slices.Contains(options, includeZeroValues) {
 			return dyn.NilValue, nil
 		}
 		return dyn.V(src.Bool()), nil
@@ -251,7 +259,7 @@ func fromTypedInt(src reflect.Value, ref dyn.Value, options ...fromTypedOptions)
 	case dyn.KindNil:
 		// This field is not set in the reference. We set it to nil if it's zero
 		// valued in the typed representation and the includeZeroValues option is not set.
-		if src.IsZero() && !slices.Contains(options, includeZeroValuedScalars) {
+		if src.IsZero() && !slices.Contains(options, includeZeroValues) {
 			return dyn.NilValue, nil
 		}
 		return dyn.V(src.Int()), nil
@@ -276,7 +284,7 @@ func fromTypedFloat(src reflect.Value, ref dyn.Value, options ...fromTypedOption
 	case dyn.KindNil:
 		// This field is not set in the reference. We set it to nil if it's zero
 		// valued in the typed representation and the includeZeroValues option is not set.
-		if src.IsZero() && !slices.Contains(options, includeZeroValuedScalars) {
+		if src.IsZero() && !slices.Contains(options, includeZeroValues) {
 			return dyn.NilValue, nil
 		}
 		return dyn.V(src.Float()), nil
diff --git a/libs/dyn/convert/from_typed_test.go b/libs/dyn/convert/from_typed_test.go
index 7a0dad84..e5447fe8 100644
--- a/libs/dyn/convert/from_typed_test.go
+++ b/libs/dyn/convert/from_typed_test.go
@@ -15,9 +15,14 @@ func TestFromTypedStructZeroFields(t *testing.T) {
 	}
 
 	src := Tmp{}
-	ref := dyn.NilValue
 
-	nv, err := FromTyped(src, ref)
+	// For an empty struct with a nil reference we expect a nil.
+	nv, err := FromTyped(src, dyn.NilValue)
+	require.NoError(t, err)
+	assert.Equal(t, dyn.NilValue, nv)
+
+	// For an empty struct with a non-nil reference we expect an empty map.
+	nv, err = FromTyped(src, dyn.V(map[string]dyn.Value{}))
 	require.NoError(t, err)
 	assert.Equal(t, dyn.V(map[string]dyn.Value{}), nv)
 }
@@ -28,17 +33,54 @@ func TestFromTypedStructPointerZeroFields(t *testing.T) {
 		Bar string `json:"bar"`
 	}
 
-	// For an initialized pointer we expect an empty map.
-	src := &Tmp{}
-	nv, err := FromTyped(src, dyn.NilValue)
-	require.NoError(t, err)
-	assert.Equal(t, dyn.V(map[string]dyn.Value{}), nv)
+	var src *Tmp
+	var nv dyn.Value
+	var err error
 
-	// For a nil pointer we expect nil.
+	// For a nil pointer with a nil reference we expect a nil.
 	src = nil
 	nv, err = FromTyped(src, dyn.NilValue)
 	require.NoError(t, err)
 	assert.Equal(t, dyn.NilValue, nv)
+
+	// For a nil pointer with a non-nil reference we expect a nil.
+	src = nil
+	nv, err = FromTyped(src, dyn.V(map[string]dyn.Value{}))
+	require.NoError(t, err)
+	assert.Equal(t, dyn.NilValue, nv)
+
+	// For an initialized pointer with a nil reference we expect a nil.
+	src = &Tmp{}
+	nv, err = FromTyped(src, dyn.NilValue)
+	require.NoError(t, err)
+	assert.Equal(t, dyn.V(map[string]dyn.Value{}), nv)
+
+	// For an initialized pointer with a non-nil reference we expect an empty map.
+	src = &Tmp{}
+	nv, err = FromTyped(src, dyn.V(map[string]dyn.Value{}))
+	require.NoError(t, err)
+	assert.Equal(t, dyn.V(map[string]dyn.Value{}), nv)
+}
+
+func TestFromTypedStructNilFields(t *testing.T) {
+	type Tmp struct {
+		Foo string `json:"foo"`
+		Bar string `json:"bar"`
+	}
+
+	// For a zero value struct with a reference containing nil fields we expect the nils to be retained.
+	src := Tmp{}
+	ref := dyn.V(map[string]dyn.Value{
+		"foo": dyn.NilValue,
+		"bar": dyn.NilValue,
+	})
+
+	nv, err := FromTyped(src, ref)
+	require.NoError(t, err)
+	assert.Equal(t, dyn.V(map[string]dyn.Value{
+		"foo": dyn.NilValue,
+		"bar": dyn.NilValue,
+	}), nv)
 }
 
 func TestFromTypedStructSetFields(t *testing.T) {