### 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
icon->set_texture(gui_base->get_theme_icon(SNAME("Folder"), SNAME("EditorIcons")));
		} else {
			label->set_text(p_paths[i].get_file());
			icon->set_texture(gui_base->get_theme_icon(SNAME("File"), SNAME("EditorIcons")));
		}
		icon->set_stretch_mode(TextureRect::STRETCH_KEEP_CENTERED);
		icon->set_size(Size2(16, 16));
		hbox->add_child(icon);
		hbox->add_child(label);
		vbox->add_child(hbox);
	}
	if (p_paths.size() > num_rows) {
		Label *label = memnew(Label);
		if (has_file && has_folder) {
			label->set_text(vformat(TTR("%d more files or folders"), p_paths.size() - num_rows));
		} else if (has_folder) {
			label->set_text(vformat(TTR("%d more folders"), p_paths.size() - num_rows));
		} else {
			label->set_text(vformat(TTR("%d more files"), p_paths.size() - num_rows));
		}
		vbox->add_child(label);
	}
	p_from->set_drag_preview(vbox); 
	Dictionary drag_data;
	drag_data["type"] = has_folder ? "files_and_dirs" : "files";
	drag_data["files"] = p_paths;
	drag_data["from"] = p_from;
	return drag_data;
}
void EditorNode::add_tool_menu_item(const String &p_name, const Callable &p_callback) {