### 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
switch (tool_menu->get_item_id(p_idx)) {
		case TOOLS_ORPHAN_RESOURCES: {
			orphan_resources->show();
		} break;
		case TOOLS_CUSTOM: {
			if (tool_menu->get_item_submenu(p_idx) == "") {
				Callable callback = tool_menu->get_item_metadata(p_idx);
				Callable::CallError ce;
				Variant result;
				callback.callp(nullptr, 0, result, ce);
				if (ce.error != Callable::CallError::CALL_OK) {
					String err = Variant::get_callable_error_text(callback, nullptr, 0, ce);
					ERR_PRINT("Error calling function from tool menu: " + err);
				}
			} 
		} break;
	}
}
void EditorNode::_export_as_menu_option(int p_idx) {