### 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)
int get_scene_tile_id(int p_index) { return get_alternative_tile_id(Vector2i(), p_index); };
	bool has_scene_tile_id(int p_id) { return has_alternative_tile(Vector2i(), p_id); };
	int create_scene_tile(Ref<PackedScene> p_packed_scene = Ref<PackedScene>(), int p_id_override = -1);
	void set_scene_tile_id(int p_id, int p_new_id);
	void set_scene_tile_scene(int p_id, Ref<PackedScene> p_packed_scene);
	Ref<PackedScene> get_scene_tile_scene(int p_id) const;
	void set_scene_tile_display_placeholder(int p_id, bool p_packed_scene);
	bool get_scene_tile_display_placeholder(int p_id) const;
	void remove_scene_tile(int p_id);
	int get_next_scene_tile_id() const;
};
class TileData : public Object {
	GDCLASS(TileData, Object);
private:
	const TileSet *tile_set = nullptr;
	bool allow_transform = true;
	
	bool flip_h = false;
	bool flip_v = false;
	bool transpose = false;
	Vector2i texture_origin;
	Ref<Material> material = Ref<Material>();
	Color modulate = Color(1.0, 1.0, 1.0, 1.0);
	int z_index = 0;
	int y_sort_origin = 0;
	Vector<Ref<OccluderPolygon2D>> occluders;