### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
ERR_FAIL_COND(!scenes.has(p_id));
	if (p_packed_scene.is_valid()) {
		
		Ref<SceneState> scene_state = p_packed_scene->get_state();
		String type;
		while (scene_state.is_valid() && type.is_empty()) {
			
			ERR_FAIL_COND(scene_state->get_node_count() < 1);
			type = scene_state->get_node_type(0);
			scene_state = scene_state->get_base_scene_state();
		}
		ERR_FAIL_COND_EDMSG(type.is_empty(), vformat("Invalid PackedScene for TileSetScenesCollectionSource: %s. Could not get the type of the root node.", p_packed_scene->get_path()));
		bool extends_correct_class = ClassDB::is_parent_class(type, "CanvasItem");
		ERR_FAIL_COND_EDMSG(!extends_correct_class, vformat("Invalid PackedScene for TileSetScenesCollectionSource: %s. Root node should extend CanvasItem. Found %s instead.", p_packed_scene->get_path(), type));
		scenes[p_id].scene = p_packed_scene;
	} else {
		scenes[p_id].scene = Ref<PackedScene>();
	}
	emit_signal(SNAME("changed"));
}
Ref<PackedScene> TileSetScenesCollectionSource::get_scene_tile_scene(int p_id) const {