### 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
ERR_FAIL_COND_V(!p_object, StringName());
	Ref<Script> scr = p_object->get_script();
	if (scr.is_null() && Object::cast_to<Script>(p_object)) {
		scr = p_object;
	}
	if (scr.is_valid()) {
		Ref<Script> base_scr = scr;
		while (base_scr.is_valid()) {
			StringName name = EditorNode::get_editor_data().script_class_get_name(base_scr->get_path());
			if (name != StringName()) {
				return name;
			}
			
			StringName base = base_scr->get_instance_base_type();
			if (base != StringName() && EditorNode::get_editor_data().get_custom_types().has(base)) {
				const Vector<EditorData::CustomType> &types = EditorNode::get_editor_data().get_custom_types()[base];
				for (int i = 0; i < types.size(); ++i) {
					if (types[i].script == base_scr) {
						return types[i].name;
					}
				}
			}
			base_scr = base_scr->get_base_script();
		}
	}
	return StringName();
}
void EditorNode::_pick_main_scene_custom_action(const String &p_custom_action_name) {