### 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
exiting = true;
	if (project_run_bar->is_playing()) {
		project_run_bar->stop_playing();
	}
	String to_reopen;
	if (get_tree()->get_edited_scene_root()) {
		to_reopen = get_tree()->get_edited_scene_root()->get_scene_file_path();
	}
	_exit_editor(EXIT_SUCCESS);
	List<String> args;
	for (const String &a : Main::get_forwardable_cli_arguments(Main::CLI_SCOPE_TOOL)) {
		args.push_back(a);
	}
	args.push_back("--path");
	args.push_back(ProjectSettings::get_singleton()->get_resource_path());
	args.push_back("-e");
	if (!to_reopen.is_empty()) {
		args.push_back(to_reopen);
	}
	OS::get_singleton()->set_restart_on_exit(true, args);
}
void EditorNode::_save_all_scenes() {