### 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
pick_main_scene->set_meta("from_native", p_from_native); 
	String main_scene = GLOBAL_GET("application/run/main_scene");
	if (main_scene.is_empty()) {
		current_menu_option = -1;
		pick_main_scene->set_text(TTR("No main scene has ever been defined, select one?\nYou can change it later in \"Project Settings\" under the 'application' category."));
		pick_main_scene->popup_centered();
		if (editor_data.get_edited_scene_root()) {
			select_current_scene_button->set_disabled(false);
			select_current_scene_button->grab_focus();
		} else {
			select_current_scene_button->set_disabled(true);
		}
		return false;
	}
	if (!FileAccess::exists(main_scene)) {
		current_menu_option = -1;
		pick_main_scene->set_text(vformat(TTR("Selected scene '%s' does not exist, select a valid one?\nYou can change it later in \"Project Settings\" under the 'application' category."), main_scene));
		pick_main_scene->popup_centered();
		return false;
	}
	if (ResourceLoader::get_resource_type(main_scene) != "PackedScene") {
		current_menu_option = -1;
		pick_main_scene->set_text(vformat(TTR("Selected scene '%s' is not a scene file, select a valid one?\nYou can change it later in \"Project Settings\" under the 'application' category."), main_scene));
		pick_main_scene->popup_centered();
		return false;
	}
	return true;
}
void EditorNode::_immediate_dialog_confirmed() {