### 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
TileSetAtlasSourceEditor::AtlasTileProxyObject *atlas_tile_proxy_object = Object::cast_to<TileSetAtlasSourceEditor::AtlasTileProxyObject>(get_edited_object());
	ERR_FAIL_COND(!atlas_tile_proxy_object);
	ERR_FAIL_COND(atlas_tile_proxy_object->get_edited_tiles().is_empty());
	Ref<TileSetAtlasSource> tile_set_atlas_source = atlas_tile_proxy_object->get_edited_tile_set_atlas_source();
	generic_tile_polygon_editor->set_tile_set(Ref<TileSet>(tile_set_atlas_source->get_tile_set()));
	
	Vector2i coords = atlas_tile_proxy_object->get_edited_tiles().front()->get().tile;
	int alternative = atlas_tile_proxy_object->get_edited_tiles().front()->get().alternative;
	TileData *tile_data = tile_set_atlas_source->get_tile_data(coords, alternative);
	generic_tile_polygon_editor->set_background(tile_set_atlas_source->get_texture(), tile_set_atlas_source->get_tile_texture_region(coords), tile_data->get_texture_origin(), tile_data->get_flip_h(), tile_data->get_flip_v(), tile_data->get_transpose(), tile_data->get_modulate());
	
	generic_tile_polygon_editor->clear_polygons();
	if (String(count_property).is_empty()) {
		if (base_type == "OccluderPolygon2D") {
			
			Ref<OccluderPolygon2D> occluder = get_edited_property_value();
			generic_tile_polygon_editor->clear_polygons();
			if (occluder.is_valid()) {
				generic_tile_polygon_editor->add_polygon(occluder->get_polygon());
			}
		} else if (base_type == "NavigationPolygon") {
			
			Ref<NavigationPolygon> navigation_polygon = get_edited_property_value();
			generic_tile_polygon_editor->clear_polygons();