### 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)
}
			undo_redo->add_undo_method(base_control, "queue_redraw");
			undo_redo->add_undo_method(this, "emit_signal", "polygons_changed");
			undo_redo->commit_action(true);
		} break;
		default:
			break;
	}
	if (!use_undo_redo) {
		memdelete(undo_redo);
	}
}
void GenericTilePolygonEditor::_grab_polygon_point(Vector2 p_pos, const Transform2D &p_polygon_xform, int &r_polygon_index, int &r_point_index) {
	const real_t grab_threshold = EDITOR_GET("editors/polygon_editor/point_grab_radius");
	r_polygon_index = -1;
	r_point_index = -1;
	float closest_distance = grab_threshold + 1.0;
	for (unsigned int i = 0; i < polygons.size(); i++) {
		const Vector<Vector2> &polygon = polygons[i];
		for (int j = 0; j < polygon.size(); j++) {
			float distance = p_pos.distance_to(p_polygon_xform.xform(polygon[j]));
			if (distance < grab_threshold && distance < closest_distance) {
				r_polygon_index = i;
				r_point_index = j;
				closest_distance = distance;
			}
		}
	}
}
void GenericTilePolygonEditor::_grab_polygon_segment_point(Vector2 p_pos, const Transform2D &p_polygon_xform, int &r_polygon_index, int &r_segment_index, Vector2 &r_point) {