### Godot version

3.5.2.stable, 4.0.1.stable

### System information

Arch Linux

### Issue description

When the `Show Hidden Files` property is enabled in the Editor Settings:
![image](https://user-images.githubusercontent.com/6501975/226908540-8e70e520-3dcd-46e4-beaf-103ac176c1de.png)
Any `FileDialog` nodes from the project will inherit this setting, and their `Show Hidden Files` property is set to true everytime the scene is re-opened:

https://user-images.githubusercontent.com/6501975/226909135-a8fafdf7-ca36-40aa-b69a-a7baf2d7ae4f.mp4


This occurs on 3.5.2 as well.

### Steps to reproduce

- Enable `Show Hidden Files` property in the Editor Settings:
    - Reload Godot for the bug to occur
- Create a FileDialog node, and set it's `Show Hidden Files` property to false
- Save and close the scene, and reopen it
- The `Show Hidden Files` property is reset to true.

### Minimal reproduction project

N/A
if (owner) {
					Ref<SceneState> ss_inst = owner->get_scene_instance_state();
					if (ss_inst.is_valid()) {
						ss_inst->update_instance_resource(p_instance_path, current_packed_scene);
					}
					owner->set_editable_instance(instantiated_node, is_editable);
				}
				
				for (AdditiveNodeEntry additive_node_entry : addition_list) {
					Node *parent_node = instantiated_node->get_node_or_null(additive_node_entry.parent);
					if (!parent_node) {
						parent_node = current_edited_scene;
					}
					parent_node->add_child(additive_node_entry.node);
					parent_node->move_child(additive_node_entry.node, additive_node_entry.index);
					
					if (additive_node_entry.owner == original_node) {
						additive_node_entry.owner = instantiated_node;
					}
					additive_node_entry.node->set_owner(additive_node_entry.owner);
					
					{
						Node2D *node_2d = Object::cast_to<Node2D>(additive_node_entry.node);
						if (node_2d) {
							node_2d->set_transform(additive_node_entry.transform_2d);
						}
						Node3D *node_3d = Object::cast_to<Node3D>(additive_node_entry.node);
						if (node_3d) {
							node_3d->set_transform(additive_node_entry.transform_3d);
						}