### 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
ProjectSettings *ps = ProjectSettings::get_singleton();
	PackedStringArray enabled_plugins = ps->get("editor_plugins/enabled");
	for (int i = 0; i < enabled_plugins.size(); ++i) {
		if (enabled_plugins.get(i) == p_name) {
			enabled_plugins.remove_at(i);
			break;
		}
	}
	ps->set("editor_plugins/enabled", enabled_plugins);
}
void EditorNode::_plugin_over_edit(EditorPlugin *p_plugin, Object *p_object) {
	if (p_object) {
		editor_plugins_over->add_plugin(p_plugin);
		p_plugin->make_visible(true);
		p_plugin->edit(p_object);
	} else {
		editor_plugins_over->remove_plugin(p_plugin);
		p_plugin->make_visible(false);
		p_plugin->edit(nullptr);
	}
}
void EditorNode::_resources_changed(const Vector<String> &p_resources) {