### 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_tile_shape(TileShape p_shape);
	TileShape get_tile_shape() const;
	void set_tile_layout(TileLayout p_layout);
	TileLayout get_tile_layout() const;
	void set_tile_offset_axis(TileOffsetAxis p_alignment);
	TileOffsetAxis get_tile_offset_axis() const;
	void set_tile_size(Size2i p_size);
	Size2i get_tile_size() const;
	
	int get_next_source_id() const;
	int get_source_count() const;
	int get_source_id(int p_index) const;
	int add_source(Ref<TileSetSource> p_tile_set_source, int p_source_id_override = -1);
	void set_source_id(int p_source_id, int p_new_id);
	void remove_source(int p_source_id);
	void remove_source_ptr(TileSetSource *p_tile_set_source); 
	bool has_source(int p_source_id) const;
	Ref<TileSetSource> get_source(int p_source_id) const;
	
	void set_uv_clipping(bool p_uv_clipping);
	bool is_uv_clipping() const;
	int get_occlusion_layers_count() const;
	void add_occlusion_layer(int p_index = -1);
	void move_occlusion_layer(int p_from_index, int p_to_pos);
	void remove_occlusion_layer(int p_index);
	void set_occlusion_layer_light_mask(int p_layer_index, int p_light_mask);
	int get_occlusion_layer_light_mask(int p_layer_index) const;
	void set_occlusion_layer_sdf_collision(int p_layer_index, bool p_sdf_collision);