### 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)
Ref<PackedScene> packed_scene = scenes_collection_source->get_scene_tile_scene(c.alternative_tile);
				if (packed_scene.is_valid()) {
					Node *scene = packed_scene->instantiate();
					Control *scene_as_control = Object::cast_to<Control>(scene);
					Node2D *scene_as_node2d = Object::cast_to<Node2D>(scene);
					if (scene_as_control) {
						scene_as_control->set_position(tile_map_node->map_to_local(r_cell_data.coords) + scene_as_control->get_position());
					} else if (scene_as_node2d) {
						Transform2D xform;
						xform.set_origin(tile_map_node->map_to_local(r_cell_data.coords));
						scene_as_node2d->set_transform(xform * scene_as_node2d->get_transform());
					}
					tile_map_node->add_child(scene);
					r_cell_data.scene = scene->get_name();
				}
			}
		}
	}
}
#ifdef DEBUG_ENABLED
void TileMapLayer::_scenes_draw_cell_debug(const RID &p_canvas_item, const Vector2i &p_quadrant_pos, const CellData &r_cell_data) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	if (!Engine::get_singleton()->is_editor_hint()) {
		return;
	}
	
	RenderingServer *rs = RenderingServer::get_singleton();
	const TileMapCell &c = r_cell_data.cell;
	TileSetSource *source;