### 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
Array rc = EditorSettings::get_singleton()->get_project_metadata("recent_files", "scenes", Array());
	recent_scenes->clear();
	String path;
	for (int i = 0; i < rc.size(); i++) {
		path = rc[i];
		recent_scenes->add_item(path.replace("res:", ""), i);
	}
	recent_scenes->add_separator();
	recent_scenes->add_shortcut(ED_SHORTCUT("editor/clear_recent", TTR("Clear Recent Scenes")));
	recent_scenes->reset_size();
}
void EditorNode::_quick_opened() {
	Vector<String> files = quick_open->get_selected_files();
	bool open_scene_dialog = quick_open->get_base_type() == "PackedScene";
	for (int i = 0; i < files.size(); i++) {
		String res_path = files[i];
		List<String> scene_extensions;
		ResourceLoader::get_recognized_extensions_for_type("PackedScene", &scene_extensions);
		if (open_scene_dialog || scene_extensions.find(files[i].get_extension().to_lower())) {
			open_request(res_path);
		} else {
			load_resource(res_path);
		}
	}
}
void EditorNode::_project_run_started() {