### 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
case Variant::ARRAY: {
				Array varray = obj->get(E.name);
				int len = varray.size();
				for (int i = 0; i < len; i++) {
					const Variant &v = varray.get(i);
					Ref<Resource> res = v;
					if (_find_and_save_resource(res, processed, flags)) {
						ret_changed = true;
					}
				}
			} break;
			case Variant::DICTIONARY: {
				Dictionary d = obj->get(E.name);
				List<Variant> keys;
				d.get_key_list(&keys);
				for (const Variant &F : keys) {
					Variant v = d[F];
					Ref<Resource> res = v;
					if (_find_and_save_resource(res, processed, flags)) {
						ret_changed = true;
					}
				}
			} break;
			default: {
			}
		}
	}
	return ret_changed;
}
void EditorNode::_save_edited_subresources(Node *scene, HashMap<Ref<Resource>, bool> &processed, int32_t flags) {