### Godot version

4.0 9f68d06

### System information

Windows 10 x64

### Issue description

When changing any property of tile source, e.g. name:
![image](https://user-images.githubusercontent.com/2223172/219977766-9babbd6c-cd75-41a0-a167-fe6da039d05e.png)
This error appears in the output:
```
UndoRedo history mismatch: expected 0, got 2.
Set name
```
It means that there is an undo action that starts with a global object and continues with a scene one.

Only happens when the TileSet is built-in and it makes the changes to the tileset being registered as global, i.e. not related to its scene (which results in history inconsistency after closing the scene).

I did some debugging and the action comes from inspector, which edits TileSetAtlasSourceEditor and then TileSetAtlasSource. I don't know what exactly triggers it; the properties should be only set on TileSetAtlasSource.

### Steps to reproduce

1. Add scene
2. Add tilemap
3. Add tileset (don't save it to a file)
4. Edit tileset
5. Add atlas source (e.g. drop icon.svg)
6. Change atlas name
7. Observe output

### Minimal reproduction project

N/A
if (singleton->exiting) {
		return;
	}
	ERR_FAIL_COND_MSG(!singleton->editor_data.has_extension_editor_plugin(p_class_name), vformat("No editor plugin added for class: %s", p_class_name));
	EditorPlugin *plugin = singleton->editor_data.get_extension_editor_plugin(p_class_name);
	remove_editor_plugin(plugin);
	memfree(plugin);
	singleton->editor_data.remove_extension_editor_plugin(p_class_name);
}
void EditorNode::_update_addon_config() {
	if (_initializing_plugins) {
		return;
	}
	Vector<String> enabled_addons;
	for (const KeyValue<String, EditorPlugin *> &E : addon_name_to_plugin) {
		enabled_addons.push_back(E.key);
	}
	if (enabled_addons.size() == 0) {
		ProjectSettings::get_singleton()->set("editor_plugins/enabled", Variant());
	} else {
		enabled_addons.sort();
		ProjectSettings::get_singleton()->set("editor_plugins/enabled", enabled_addons);
	}
	project_settings_editor->queue_save();
}
void EditorNode::set_addon_plugin_enabled(const String &p_addon, bool p_enabled, bool p_config_changed) {