### 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
switch (current_menu_option) {
		case FILE_NEW_INHERITED_SCENE: {
			Node *scene = editor_data.get_edited_scene_root();
			
			if (!scene) {
				_menu_option_confirm(FILE_CLOSE, true);
			}
			load_scene(p_file, false, true);
		} break;
		case FILE_OPEN_SCENE: {
			load_scene(p_file);
		} break;
		case SETTINGS_PICK_MAIN_SCENE: {
			ProjectSettings::get_singleton()->set("application/run/main_scene", p_file);
			ProjectSettings::get_singleton()->save();
			
			project_run_bar->play_main_scene((bool)pick_main_scene->get_meta("from_native", false));
		} break;
		case FILE_CLOSE:
		case SCENE_TAB_CLOSE:
		case FILE_SAVE_SCENE:
		case FILE_SAVE_AS_SCENE: {