### 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)
Node *node = tile_map_node->get_node_or_null(r_cell_data.scene);
	if (node) {
		node->queue_free();
	}
	r_cell_data.scene = "";
}
void TileMapLayer::_scenes_update_cell(CellData &r_cell_data) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	
	_scenes_clear_cell(r_cell_data);
	
	const 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)) {
			TileSetScenesCollectionSource *scenes_collection_source = Object::cast_to<TileSetScenesCollectionSource>(source);
			if (scenes_collection_source) {