### 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)
void set_texture(Ref<Texture2D> p_texture);
	Ref<Texture2D> get_texture() const;
	void set_margins(Vector2i p_margins);
	Vector2i get_margins() const;
	void set_separation(Vector2i p_separation);
	Vector2i get_separation() const;
	void set_texture_region_size(Vector2i p_tile_size);
	Vector2i get_texture_region_size() const;
	
	void set_use_texture_padding(bool p_use_padding);
	bool get_use_texture_padding() const;
	
	void create_tile(const Vector2i p_atlas_coords, const Vector2i p_size = Vector2i(1, 1));
	void remove_tile(Vector2i p_atlas_coords);
	virtual bool has_tile(Vector2i p_atlas_coords) const override;
	void move_tile_in_atlas(Vector2i p_atlas_coords, Vector2i p_new_atlas_coords = INVALID_ATLAS_COORDS, Vector2i p_new_size = Vector2i(-1, -1));
	Vector2i get_tile_size_in_atlas(Vector2i p_atlas_coords) const;
	virtual int get_tiles_count() const override;
	virtual Vector2i get_tile_id(int p_index) const override;
	bool has_room_for_tile(Vector2i p_atlas_coords, Vector2i p_size, int p_animation_columns, Vector2i p_animation_separation, int p_frames_count, Vector2i p_ignored_tile = INVALID_ATLAS_COORDS) const;
	PackedVector2Array get_tiles_to_be_removed_on_change(Ref<Texture2D> p_texture, Vector2i p_margins, Vector2i p_separation, Vector2i p_texture_region_size);
	Vector2i get_tile_at_coords(Vector2i p_atlas_coords) const;
	bool has_tiles_outside_texture() const;
	Vector<Vector2i> get_tiles_outside_texture() const;
	void clear_tiles_outside_texture();
	
	void set_tile_animation_columns(const Vector2i p_atlas_coords, int p_frame_columns);
	int get_tile_animation_columns(const Vector2i p_atlas_coords) const;
	void set_tile_animation_separation(const Vector2i p_atlas_coords, const Vector2i p_separation);
	Vector2i get_tile_animation_separation(const Vector2i p_atlas_coords) const;