### 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)
const real_t grab_threshold = EDITOR_GET("editors/polygon_editor/point_grab_radius");
	Point2 point = p_polygon_xform.affine_inverse().xform(p_pos);
	r_polygon_index = -1;
	r_segment_index = -1;
	float closest_distance = grab_threshold * 2.0;
	for (unsigned int i = 0; i < polygons.size(); i++) {
		const Vector<Vector2> &polygon = polygons[i];
		for (int j = 0; j < polygon.size(); j++) {
			Vector2 segment[2] = { polygon[j], polygon[(j + 1) % polygon.size()] };
			Vector2 closest_point = Geometry2D::get_closest_point_to_segment(point, segment);
			float distance = closest_point.distance_to(point);
			if (distance < grab_threshold / editor_zoom_widget->get_zoom() && distance < closest_distance) {
				r_polygon_index = i;
				r_segment_index = j;
				r_point = closest_point;
				closest_distance = distance;
			}
		}
	}
}
void GenericTilePolygonEditor::_snap_to_tile_shape(Point2 &r_point, float &r_current_snapped_dist, float p_snap_dist) {