### 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)
#ifndef DISABLE_DEPRECATED
	ClassDB::bind_method(D_METHOD("set_navigation_map", "layer", "map"), &TileMap::set_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("get_navigation_map", "layer"), &TileMap::get_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("force_update", "layer"), &TileMap::force_update, DEFVAL(-1));
#endif 
	ClassDB::bind_method(D_METHOD("set_tileset", "tileset"), &TileMap::set_tileset);
	ClassDB::bind_method(D_METHOD("get_tileset"), &TileMap::get_tileset);
	ClassDB::bind_method(D_METHOD("set_rendering_quadrant_size", "size"), &TileMap::set_rendering_quadrant_size);
	ClassDB::bind_method(D_METHOD("get_rendering_quadrant_size"), &TileMap::get_rendering_quadrant_size);
	ClassDB::bind_method(D_METHOD("get_layers_count"), &TileMap::get_layers_count);
	ClassDB::bind_method(D_METHOD("add_layer", "to_position"), &TileMap::add_layer);
	ClassDB::bind_method(D_METHOD("move_layer", "layer", "to_position"), &TileMap::move_layer);
	ClassDB::bind_method(D_METHOD("remove_layer", "layer"), &TileMap::remove_layer);
	ClassDB::bind_method(D_METHOD("set_layer_name", "layer", "name"), &TileMap::set_layer_name);
	ClassDB::bind_method(D_METHOD("get_layer_name", "layer"), &TileMap::get_layer_name);
	ClassDB::bind_method(D_METHOD("set_layer_enabled", "layer", "enabled"), &TileMap::set_layer_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_enabled", "layer"), &TileMap::is_layer_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_modulate", "layer", "modulate"), &TileMap::set_layer_modulate);
	ClassDB::bind_method(D_METHOD("get_layer_modulate", "layer"), &TileMap::get_layer_modulate);
	ClassDB::bind_method(D_METHOD("set_layer_y_sort_enabled", "layer", "y_sort_enabled"), &TileMap::set_layer_y_sort_enabled);
	ClassDB::bind_method(D_METHOD("is_layer_y_sort_enabled", "layer"), &TileMap::is_layer_y_sort_enabled);
	ClassDB::bind_method(D_METHOD("set_layer_y_sort_origin", "layer", "y_sort_origin"), &TileMap::set_layer_y_sort_origin);