### 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
ERR_FAIL_NULL(p_editing_owner);
	if (p_object && _is_class_editor_disabled_by_feature_profile(p_object->get_class())) {
		return;
	}
	Vector<EditorPlugin *> item_plugins;
	if (p_object) {
		item_plugins = editor_data.get_subeditors(p_object);
	}
	if (!item_plugins.is_empty()) {
		ObjectID owner_id = p_editing_owner->get_instance_id();
		List<EditorPlugin *> to_remove;
		for (EditorPlugin *plugin : active_plugins[owner_id]) {
			if (!item_plugins.has(plugin)) {
				
				to_remove.push_back(plugin);
				_plugin_over_edit(plugin, nullptr);
			}
		}
		for (EditorPlugin *plugin : to_remove) {
			active_plugins[owner_id].erase(plugin);