### 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)
const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	TileMapCell &c = r_cell_data.cell;
	TileSetSource *source;
	if (tile_set->has_source(c.source_id)) {
		source = *tile_set->get_source(c.source_id);
		if (source->has_tile(c.get_atlas_coords()) && source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				bool ret = false;
				if (tile_map_node->GDVIRTUAL_CALL(_use_tile_data_runtime_update, layer_index_in_tile_map_node, r_cell_data.coords, ret) && ret) {
					TileData *tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
					
					TileData *tile_data_runtime_use = tile_data->duplicate();
					tile_data_runtime_use->set_allow_transform(true);
					r_cell_data.runtime_tile_data_cache = tile_data_runtime_use;
					tile_map_node->GDVIRTUAL_CALL(_tile_data_runtime_update, layer_index_in_tile_map_node, r_cell_data.coords, tile_data_runtime_use);
					if (p_auto_add_to_dirty_list) {
						dirty.cell_list.add(&r_cell_data.dirty_list_element);
					}
				}
			}
		}
	}
}
void TileMapLayer::_clear_runtime_update_tile_data() {