### 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)
return layers.size();
}
void TileMap::add_layer(int p_to_pos) {
	if (p_to_pos < 0) {
		p_to_pos = layers.size() + p_to_pos + 1;
	}
	ERR_FAIL_INDEX(p_to_pos, (int)layers.size() + 1);
	
	Ref<TileMapLayer> new_layer;
	new_layer.instantiate();
	new_layer->set_tile_map(this);
	layers.insert(p_to_pos, new_layer);
	for (uint32_t i = 0; i < layers.size(); i++) {
		layers[i]->set_layer_index_in_tile_map_node(i);
	}
	queue_internal_update();
	notify_property_list_changed();
	emit_signal(CoreStringNames::get_singleton()->changed);
	update_configuration_warnings();
}
void TileMap::move_layer(int p_layer, int p_to_pos) {