### 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
int idx = tool_menu->get_item_count();
	tool_menu->add_item(p_name, TOOLS_CUSTOM);
	tool_menu->set_item_metadata(idx, p_callback);
}
void EditorNode::add_tool_submenu_item(const String &p_name, PopupMenu *p_submenu) {
	ERR_FAIL_NULL(p_submenu);
	ERR_FAIL_COND(p_submenu->get_parent() != nullptr);
	tool_menu->add_child(p_submenu);
	tool_menu->add_submenu_item(p_name, p_submenu->get_name(), TOOLS_CUSTOM);
}
void EditorNode::remove_tool_menu_item(const String &p_name) {
	for (int i = 0; i < tool_menu->get_item_count(); i++) {
		if (tool_menu->get_item_id(i) != TOOLS_CUSTOM) {
			continue;
		}
		if (tool_menu->get_item_text(i) == p_name) {
			if (tool_menu->get_item_submenu(i) != "") {
				Node *n = tool_menu->get_node(tool_menu->get_item_submenu(i));
				tool_menu->remove_child(n);
				memdelete(n);
			}
			tool_menu->remove_item(i);
			tool_menu->reset_size();
			return;
		}
	}
}
PopupMenu *EditorNode::get_export_as_menu() {