### 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)
polygon_cache[Pair<Ref<Resource>, int>(p_polygon, p_alternative_id)] = ret;
		return ret;
	}
	Ref<NavigationPolygon> nav = p_polygon;
	if (nav.is_valid()) {
		PackedVector2Array new_points = _get_transformed_vertices(nav->get_vertices(), p_alternative_id);
		Ref<NavigationPolygon> ret;
		ret.instantiate();
		ret->set_vertices(new_points);
		PackedInt32Array indices;
		indices.resize(new_points.size());
		int *w = indices.ptrw();
		for (int i = 0; i < new_points.size(); i++) {
			w[i] = i;
		}
		ret->add_polygon(indices);
		polygon_cache[Pair<Ref<Resource>, int>(p_polygon, p_alternative_id)] = ret;
		return ret;
	}
	Ref<OccluderPolygon2D> ocd = p_polygon;
	if (ocd.is_valid()) {
		Ref<OccluderPolygon2D> ret;
		ret.instantiate();
		ret->set_polygon(_get_transformed_vertices(ocd->get_polygon(), p_alternative_id));
		polygon_cache[Pair<Ref<Resource>, int>(p_polygon, p_alternative_id)] = ret;
		return ret;
	}
	return p_polygon;
}
PackedStringArray TileMap::get_configuration_warnings() const {