### 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_navigation_layers_count() const;
	void add_navigation_layer(int p_index = -1);
	void move_navigation_layer(int p_from_index, int p_to_pos);
	void remove_navigation_layer(int p_index);
	void set_navigation_layer_layers(int p_layer_index, uint32_t p_layers);
	uint32_t get_navigation_layer_layers(int p_layer_index) const;
	void set_navigation_layer_layer_value(int p_layer_index, int p_layer_number, bool p_value);
	bool get_navigation_layer_layer_value(int p_layer_index, int p_layer_number) const;
	
	int get_custom_data_layers_count() const;
	void add_custom_data_layer(int p_index = -1);
	void move_custom_data_layer(int p_from_index, int p_to_pos);
	void remove_custom_data_layer(int p_index);
	int get_custom_data_layer_by_name(String p_value) const;
	void set_custom_data_layer_name(int p_layer_id, String p_value);
	String get_custom_data_layer_name(int p_layer_id) const;
	void set_custom_data_layer_type(int p_layer_id, Variant::Type p_value);
	Variant::Type get_custom_data_layer_type(int p_layer_id) const;
	
	void set_source_level_tile_proxy(int p_source_from, int p_source_to);
	int get_source_level_tile_proxy(int p_source_from);
	bool has_source_level_tile_proxy(int p_source_from);
	void remove_source_level_tile_proxy(int p_source_from);
	void set_coords_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_source_to, Vector2i p_coords_to);
	Array get_coords_level_tile_proxy(int p_source_from, Vector2i p_coords_from);
	bool has_coords_level_tile_proxy(int p_source_from, Vector2i p_coords_from);
	void remove_coords_level_tile_proxy(int p_source_from, Vector2i p_coords_from);
	void set_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from, int p_source_to, Vector2i p_coords_to, int p_alternative_to);
	Array get_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from);