### 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)
base_control->draw_line(in_creation_polygon[i], in_creation_polygon[i + 1], Color(1.0, 1.0, 1.0));
		}
	}
	Point2 in_creation_point = xform.affine_inverse().xform(base_control->get_local_mouse_position());
	float in_creation_distance = grab_threshold * 2.0;
	_snap_to_tile_shape(in_creation_point, in_creation_distance, grab_threshold / editor_zoom_widget->get_zoom());
	_snap_point(in_creation_point);
	if (drag_type == DRAG_TYPE_CREATE_POINT && !in_creation_polygon.is_empty()) {
		base_control->draw_line(in_creation_polygon[in_creation_polygon.size() - 1], in_creation_point, Color(1.0, 1.0, 1.0));
	}
	
	int tinted_polygon_index = -1;
	int tinted_point_index = -1;
	if (drag_type == DRAG_TYPE_DRAG_POINT) {
		tinted_polygon_index = drag_polygon_index;
		tinted_point_index = drag_point_index;
	} else if (hovered_point_index >= 0) {
		tinted_polygon_index = hovered_polygon_index;
		tinted_point_index = hovered_point_index;
	}
	base_control->draw_set_transform_matrix(Transform2D());
	if (!in_creation_polygon.is_empty()) {
		for (int i = 0; i < in_creation_polygon.size(); i++) {
			base_control->draw_texture(handle, xform.xform(in_creation_polygon[i]) - handle->get_size() / 2);
		}
	} else {
		for (int i = 0; i < (int)polygons.size(); i++) {
			const Vector<Vector2> &polygon = polygons[i];
			for (int j = 0; j < polygon.size(); j++) {
				const Color poly_modulate = (tinted_polygon_index == i && tinted_point_index == j) ? Color(0.5, 1, 2) : Color(1, 1, 1);