### 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 (tile_meshes_dirty) {
		Vector<Vector2> shape = get_tile_shape_polygon();
		Vector<Vector2> uvs;
		uvs.resize(shape.size());
		for (int i = 0; i < shape.size(); i++) {
			uvs.write[i] = shape[i] + Vector2(0.5, 0.5);
		}
		Vector<Color> colors;
		colors.resize(shape.size());
		colors.fill(Color(1.0, 1.0, 1.0, 1.0));
		
		tile_filled_mesh->clear_surfaces();
		Array a;
		a.resize(Mesh::ARRAY_MAX);
		a[Mesh::ARRAY_VERTEX] = shape;
		a[Mesh::ARRAY_TEX_UV] = uvs;
		a[Mesh::ARRAY_COLOR] = colors;
		a[Mesh::ARRAY_INDEX] = Geometry2D::triangulate_polygon(shape);
		tile_filled_mesh->add_surface_from_arrays(Mesh::PRIMITIVE_TRIANGLES, a, Array(), Dictionary(), Mesh::ARRAY_FLAG_USE_2D_VERTICES);
		
		tile_lines_mesh->clear_surfaces();
		a.clear();
		a.resize(Mesh::ARRAY_MAX);
		
		shape.push_back(shape[0]);
		colors.push_back(colors[0]);
		a[Mesh::ARRAY_VERTEX] = shape;
		a[Mesh::ARRAY_COLOR] = colors;