### 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)
Array output;
	for (const KeyValue<Array, Array> &E : coords_level_proxies) {
		Array proxy;
		proxy.append_array(E.key);
		proxy.append_array(E.value);
		output.push_back(proxy);
	}
	return output;
}
Array TileSet::get_alternative_level_tile_proxies() const {
	Array output;
	for (const KeyValue<Array, Array> &E : alternative_level_proxies) {
		Array proxy;
		proxy.append_array(E.key);
		proxy.append_array(E.value);
		output.push_back(proxy);
	}
	return output;
}
Array TileSet::map_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) const {
	Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	from.push_back(p_alternative_from);
	
	if (has_source(p_source_from)) {
		Ref<TileSetSource> source = get_source(p_source_from);