### 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
editor_layout_save_delay_timer->start();
}
void EditorNode::_dock_split_dragged(int ofs) {
	editor_layout_save_delay_timer->start();
}
void EditorNode::_load_editor_layout() {
	Ref<ConfigFile> config;
	config.instantiate();
	Error err = config->load(EditorPaths::get_singleton()->get_project_settings_dir().path_join("editor_layout.cfg"));
	if (err != OK) { 
		
		TreeItem *root = FileSystemDock::get_singleton()->get_tree_control()->get_item_with_metadata("res:", 0);
		if (root) {
			root->set_collapsed(false);
		}
		if (overridden_default_layout >= 0) {
			_layout_menu_option(overridden_default_layout);
		}
		return;
	}
	_load_docks_from_config(config, "docks");
	_load_open_scenes_from_config(config);
	_load_central_editor_layout_from_config(config);
	editor_data.set_plugin_window_layout(config);
}
void EditorNode::_update_dock_slots_visibility(bool p_keep_selected_tabs) {