### 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
tile_data_custom_data_editor->connect("needs_redraw", callable_mp((CanvasItem *)alternative_tiles_control_unscaled, &Control::queue_redraw));
			tile_data_editors[editor_name] = tile_data_custom_data_editor;
		}
	}
	for (int i = tile_set->get_custom_data_layers_count(); tile_data_editors.has(vformat("custom_data_%d", i)); i++) {
		tile_data_editors[vformat("custom_data_%d", i)]->queue_free();
		tile_data_editors.erase(vformat("custom_data_%d", i));
	}
	if (tile_set->get_custom_data_layers_count() == 0) {
		item = tile_data_editors_tree->create_item(group);
		item->set_icon(0, get_theme_icon("Info", "EditorIcons"));
		item->set_icon_modulate(0, disabled_color);
		item->set_text(0, TTR("No custom data layers"));
		item->set_tooltip_text(0, TTR("Create and customize custom data layers in the inspector of the TileSet resource."));
		item->set_selectable(0, false);
		item->set_custom_color(0, disabled_color);
	}
#undef ADD_TILE_DATA_EDITOR_GROUP
#undef ADD_TILE_DATA_EDITOR
	
	for (KeyValue<String, TileDataEditor *> &E : tile_data_editors) {
		
		TileDataEditor *tile_data_editor = E.value;
		if (!tile_data_editor->is_inside_tree()) {
			tile_data_painting_editor_container->add_child(tile_data_editor);
		}
		tile_data_editor->set_tile_set(tile_set);
		
		Control *toolbar = tile_data_editor->get_toolbar();
		if (!toolbar->is_inside_tree()) {