### 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)
GDCLASS(TileSetScenesCollectionSource, TileSetSource);
private:
	struct SceneData {
		Ref<PackedScene> scene;
		bool display_placeholder = false;
	};
	Vector<int> scenes_ids;
	HashMap<int, SceneData> scenes;
	int next_scene_id = 1;
	void _compute_next_alternative_id();
protected:
	bool _set(const StringName &p_name, const Variant &p_value);
	bool _get(const StringName &p_name, Variant &r_ret) const;
	void _get_property_list(List<PropertyInfo> *p_list) const;
	static void _bind_methods();
public:
	
	int get_tiles_count() const override;
	Vector2i get_tile_id(int p_tile_index) const override;
	bool has_tile(Vector2i p_atlas_coords) const override;
	
	int get_alternative_tiles_count(const Vector2i p_atlas_coords) const override;
	int get_alternative_tile_id(const Vector2i p_atlas_coords, int p_index) const override;
	bool has_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_tile) const override;
	
	int get_scene_tiles_count() { return get_alternative_tiles_count(Vector2i()); }