### 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 (get_editor_data().get_edited_scene_root()) {
		if (get_editor_data().get_edited_scene_root()->get_parent() == scene_root) {
			scene_root->remove_child(get_editor_data().get_edited_scene_root());
		}
	}
	get_editor_data().set_edited_scene_root(p_scene);
	if (Object::cast_to<Popup>(p_scene)) {
		Object::cast_to<Popup>(p_scene)->show();
	}
	SceneTreeDock::get_singleton()->set_edited_scene(p_scene);
	if (get_tree()) {
		get_tree()->set_edited_scene_root(p_scene);
	}
	if (p_scene) {
		if (p_scene->get_parent() != scene_root) {
			scene_root->add_child(p_scene, true);
		}
	}
}
int EditorNode::_get_current_main_editor() {
	for (int i = 0; i < editor_table.size(); i++) {
		if (editor_table[i] == editor_plugin_screen) {
			return i;
		}
	}
	return 0;
}
Dictionary EditorNode::_get_main_scene_state() {