### 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)
for (const Vector<Vector2> &traversable_outline : traversable_outlines) {
		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);
	}
	for (const Vector<Vector2> &obstruction_outline : obstruction_outlines) {
		Path64 clip_path;
		for (const Vector2 &obstruction_point : obstruction_outline) {
			const Point64 &point = Point64(obstruction_point.x, obstruction_point.y);
			clip_path.push_back(point);
		}
		obstruction_polygon_paths.push_back(clip_path);
	}
	Paths64 path_solution;
	
	Paths64 dummy_clip_path;
	traversable_polygon_paths = Union(traversable_polygon_paths, dummy_clip_path, FillRule::NonZero);
	
	obstruction_polygon_paths = Union(obstruction_polygon_paths, dummy_clip_path, FillRule::NonZero);
	path_solution = Difference(traversable_polygon_paths, obstruction_polygon_paths, FillRule::NonZero);
	real_t agent_radius_offset = p_navigation_mesh->get_agent_radius();
	if (agent_radius_offset > 0.0) {
		path_solution = InflatePaths(path_solution, -agent_radius_offset, JoinType::Miter, EndType::Polygon);
	}
	
	Vector<Vector<Vector2>> new_baked_outlines;
	for (const Path64 &scaled_path : path_solution) {