### 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
exiting = true;
	if (project_run_bar->is_playing()) {
		project_run_bar->stop_playing();
	}
	String to_reopen;
	if (get_tree()->get_edited_scene_root()) {
		to_reopen = get_tree()->get_edited_scene_root()->get_scene_file_path();
	}
	_exit_editor(EXIT_SUCCESS);
	List<String> args;
	for (const String &a : Main::get_forwardable_cli_arguments(Main::CLI_SCOPE_TOOL)) {
		args.push_back(a);
	}
	args.push_back("--path");
	args.push_back(ProjectSettings::get_singleton()->get_resource_path());
	args.push_back("-e");
	if (!to_reopen.is_empty()) {
		args.push_back(to_reopen);
	}
	OS::get_singleton()->set_restart_on_exit(true, args);
}
void EditorNode::_save_all_scenes() {