### 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)
StaticBody2D *static_body = Object::cast_to<StaticBody2D>(p_node);
	if (static_body == nullptr) {
		return;
	}
	NavigationPolygon::ParsedGeometryType parsed_geometry_type = p_navigation_mesh->get_parsed_geometry_type();
	if (!(parsed_geometry_type == NavigationPolygon::PARSED_GEOMETRY_STATIC_COLLIDERS || parsed_geometry_type == NavigationPolygon::PARSED_GEOMETRY_BOTH)) {
		return;
	}
	uint32_t parsed_collision_mask = p_navigation_mesh->get_parsed_collision_mask();
	if (!(static_body->get_collision_layer() & parsed_collision_mask)) {
		return;
	}
	List<uint32_t> shape_owners;
	static_body->get_shape_owners(&shape_owners);
	for (uint32_t shape_owner : shape_owners) {
		if (static_body->is_shape_owner_disabled(shape_owner)) {
			continue;
		}
		const int shape_count = static_body->shape_owner_get_shape_count(shape_owner);
		for (int shape_index = 0; shape_index < shape_count; shape_index++) {
			Ref<Shape2D> s = static_body->shape_owner_get_shape(shape_owner, shape_index);
			if (s.is_null()) {
				continue;
			}
			const Transform2D static_body_xform = p_source_geometry_data->root_node_transform * static_body->get_global_transform() * static_body->shape_owner_get_transform(shape_owner);
			RectangleShape2D *rectangle_shape = Object::cast_to<RectangleShape2D>(*s);
			if (rectangle_shape) {
				Vector<Vector2> shape_outline;