### 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
pick_main_scene->set_meta("from_native", p_from_native); 
	String main_scene = GLOBAL_GET("application/run/main_scene");
	if (main_scene.is_empty()) {
		current_menu_option = -1;
		pick_main_scene->set_text(TTR("No main scene has ever been defined, select one?\nYou can change it later in \"Project Settings\" under the 'application' category."));
		pick_main_scene->popup_centered();
		if (editor_data.get_edited_scene_root()) {
			select_current_scene_button->set_disabled(false);
			select_current_scene_button->grab_focus();
		} else {
			select_current_scene_button->set_disabled(true);
		}
		return false;
	}
	if (!FileAccess::exists(main_scene)) {
		current_menu_option = -1;
		pick_main_scene->set_text(vformat(TTR("Selected scene '%s' does not exist, select a valid one?\nYou can change it later in \"Project Settings\" under the 'application' category."), main_scene));
		pick_main_scene->popup_centered();
		return false;
	}
	if (ResourceLoader::get_resource_type(main_scene) != "PackedScene") {
		current_menu_option = -1;
		pick_main_scene->set_text(vformat(TTR("Selected scene '%s' is not a scene file, select a valid one?\nYou can change it later in \"Project Settings\" under the 'application' category."), main_scene));
		pick_main_scene->popup_centered();
		return false;
	}
	return true;
}
void EditorNode::_immediate_dialog_confirmed() {