### 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)
baking_navmesh_mutex.lock();
	generator_task_mutex.lock();
	baking_navmeshes.clear();
	for (KeyValue<WorkerThreadPool::TaskID, NavMeshGeneratorTask2D *> &E : generator_tasks) {
		WorkerThreadPool::get_singleton()->wait_for_task_completion(E.key);
		NavMeshGeneratorTask2D *generator_task = E.value;
		memdelete(generator_task);
	}
	generator_tasks.clear();
	generator_task_mutex.unlock();
	baking_navmesh_mutex.unlock();
}
void NavMeshGenerator2D::finish() {
	cleanup();
}
void NavMeshGenerator2D::parse_source_geometry_data(Ref<NavigationPolygon> p_navigation_mesh, Ref<NavigationMeshSourceGeometryData2D> p_source_geometry_data, Node *p_root_node, const Callable &p_callback) {
	ERR_FAIL_COND(!Thread::is_main_thread());
	ERR_FAIL_COND(!p_navigation_mesh.is_valid());
	ERR_FAIL_NULL(p_root_node);
	ERR_FAIL_COND(!p_root_node->is_inside_tree());
	ERR_FAIL_COND(!p_source_geometry_data.is_valid());
	generator_parse_source_geometry_data(p_navigation_mesh, p_source_geometry_data, p_root_node);
	if (p_callback.is_valid()) {
		generator_emit_callback(p_callback);
	}
}
void NavMeshGenerator2D::bake_from_source_geometry_data(Ref<NavigationPolygon> p_navigation_mesh, Ref<NavigationMeshSourceGeometryData2D> p_source_geometry_data, const Callable &p_callback) {