### 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)
for (RID &ci : rendering_quadrant->canvas_items) {
					rs->free(ci);
				}
				rendering_quadrant->canvas_items.clear();
				
				if (tile_map_node->is_y_sort_enabled() && is_y_sort_enabled()) {
					
					rendering_quadrant->cells.sort_custom<CellDataYSortedComparator>();
				} else {
					rendering_quadrant->cells.sort();
				}
				
				Ref<Material> prev_material;
				int prev_z_index = 0;
				RID prev_ci;
				for (SelfList<CellData> *cell_data_quadrant_list_element = rendering_quadrant->cells.first(); cell_data_quadrant_list_element; cell_data_quadrant_list_element = cell_data_quadrant_list_element->next()) {
					CellData &cell_data = *cell_data_quadrant_list_element->self();
					TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(*tile_set->get_source(cell_data.cell.source_id));
					
					const TileData *tile_data;
					if (cell_data.runtime_tile_data_cache) {
						tile_data = cell_data.runtime_tile_data_cache;
					} else {
						tile_data = atlas_source->get_tile_data(cell_data.cell.get_atlas_coords(), cell_data.cell.alternative_tile);
					}
					Ref<Material> mat = tile_data->get_material();
					int tile_z_index = tile_data->get_z_index();