### 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)
Rect2i rect;
		rect.set_position(p_tile_atlas_view->get_atlas_tile_coords_at_pos(drag_start_pos, true));
		rect.set_end(p_tile_atlas_view->get_atlas_tile_coords_at_pos(p_transform.affine_inverse().xform(p_canvas_item->get_local_mouse_position()), true));
		rect = rect.abs();
		RBSet<TileMapCell> edited;
		for (int x = rect.get_position().x; x <= rect.get_end().x; x++) {
			for (int y = rect.get_position().y; y <= rect.get_end().y; y++) {
				Vector2i coords = Vector2i(x, y);
				coords = p_tile_set_atlas_source->get_tile_at_coords(coords);
				if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
					TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, 0);
					if (tile_data->get_terrain_set() == terrain_set) {
						TileMapCell cell;
						cell.source_id = 0;
						cell.set_atlas_coords(coords);
						cell.alternative_tile = 0;
						edited.insert(cell);
					}
				}
			}
		}
		Vector2 end = p_transform.affine_inverse().xform(p_canvas_item->get_local_mouse_position());
		Vector<Point2> mouse_pos_rect_polygon;
		mouse_pos_rect_polygon.push_back(drag_start_pos);
		mouse_pos_rect_polygon.push_back(Vector2(end.x, drag_start_pos.y));
		mouse_pos_rect_polygon.push_back(end);
		mouse_pos_rect_polygon.push_back(Vector2(drag_start_pos.x, end.y));
		Vector<Color> color;
		color.push_back(Color(1.0, 1.0, 1.0, 0.5));
		p_canvas_item->draw_set_transform_matrix(p_transform);