### 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)
PropertyInfo property_info;
	for (const KeyValue<Vector2i, TileAlternativesData> &E_tile : tiles) {
		List<PropertyInfo> tile_property_list;
		
		property_info = PropertyInfo(Variant::VECTOR2I, "size_in_atlas", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.size_in_atlas == Vector2i(1, 1)) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		tile_property_list.push_back(property_info);
		
		property_info = PropertyInfo(Variant::INT, "next_alternative_id", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.next_alternative_id == 1) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}