### 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)
if (p_navigation_mesh.is_null() || p_source_geometry_data.is_null()) {
		return;
	}
	if (p_navigation_mesh->get_outline_count() == 0 && !p_source_geometry_data->has_data()) {
		return;
	}
	int outline_count = p_navigation_mesh->get_outline_count();
	const Vector<Vector<Vector2>> &traversable_outlines = p_source_geometry_data->_get_traversable_outlines();
	const Vector<Vector<Vector2>> &obstruction_outlines = p_source_geometry_data->_get_obstruction_outlines();
	if (outline_count == 0 && traversable_outlines.size() == 0) {
		return;
	}
	using namespace Clipper2Lib;
	Paths64 traversable_polygon_paths;
	Paths64 obstruction_polygon_paths;
	for (int i = 0; i < outline_count; i++) {
		const Vector<Vector2> &traversable_outline = p_navigation_mesh->get_outline(i);
		Path64 subject_path;
		for (const Vector2 &traversable_point : traversable_outline) {
			const Point64 &point = Point64(traversable_point.x, traversable_point.y);
			subject_path.push_back(point);
		}
		traversable_polygon_paths.push_back(subject_path);
	}