### 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)
VISIBILITY_MODE_FORCE_SHOW,
		VISIBILITY_MODE_FORCE_HIDE,
	};
private:
	friend class TileSetPlugin;
	
	mutable TileMapLayer::DataFormat format = TileMapLayer::FORMAT_3;
	static constexpr float FP_ADJUST = 0.00001;
	
	Ref<TileSet> tile_set;
	int rendering_quadrant_size = 16;
	bool collision_animatable = false;
	VisibilityMode collision_visibility_mode = VISIBILITY_MODE_DEFAULT;
	VisibilityMode navigation_visibility_mode = VISIBILITY_MODE_DEFAULT;
	
	LocalVector<Ref<TileMapLayer>> layers;
	Ref<TileMapLayer> default_layer; 
	int selected_layer = -1;
	bool pending_update = false;
	Transform2D last_valid_transform;
	Transform2D new_transform;
	void _tile_set_changed();
	void _update_notify_local_transform();
	
	HashMap<Pair<Ref<Resource>, int>, Ref<Resource>, PairHash<Ref<Resource>, int>> polygon_cache;
	PackedVector2Array _get_transformed_vertices(const PackedVector2Array &p_vertices, int p_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;