### 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 (!tile_set_atlas_source) {
		return;
	}
	Ref<Texture2D> texture = tile_set_atlas_source->get_texture();
	if (texture.is_valid()) {
		Vector2i margins = tile_set_atlas_source->get_margins();
		Vector2i separation = tile_set_atlas_source->get_separation();
		Vector2i texture_region_size = tile_set_atlas_source->get_texture_region_size();
		Vector2i grid_size = tile_set_atlas_source->get_atlas_grid_size();
		EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
		undo_redo->create_action(TTR("Remove tiles in fully transparent texture regions"));
		List<PropertyInfo> list;
		tile_set_atlas_source->get_property_list(&list);
		HashMap<Vector2i, List<const PropertyInfo *>> per_tile = _group_properties_per_tiles(list, tile_set_atlas_source);
		for (int i = 0; i < tile_set_atlas_source->get_tiles_count(); i++) {
			Vector2i coords = tile_set_atlas_source->get_tile_id(i);
			Vector2i size_in_atlas = tile_set_atlas_source->get_tile_size_in_atlas(coords);
			
			if ((coords.x + size_in_atlas.x) > grid_size.x || (coords.y + size_in_atlas.y) > grid_size.y) {
				continue;
			}
			
			Rect2i region = Rect2i(margins + (coords * (texture_region_size + separation)), texture_region_size * size_in_atlas);
			bool is_opaque = false;