### 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 (waiting_for_first_scan) {
		waiting_for_first_scan = false;
		OS::get_singleton()->benchmark_end_measure("editor_scan_and_import");
		
		
		RenderingServer::get_singleton()->global_shader_parameters_load_settings(true);
		
		if (!singleton->cmdline_export_mode) {
			EditorResourcePreview::get_singleton()->start();
		}
		_load_editor_layout();
		if (!defer_load_scene.is_empty()) {
			OS::get_singleton()->benchmark_begin_measure("editor_load_scene");
			load_scene(defer_load_scene);
			defer_load_scene = "";
			OS::get_singleton()->benchmark_end_measure("editor_load_scene");
			OS::get_singleton()->benchmark_dump();
		}
	}
}
void EditorNode::_scan_external_changes() {