### 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)
bool get_occlusion_layer_sdf_collision(int p_layer_index) const;
	
	int get_physics_layers_count() const;
	void add_physics_layer(int p_index = -1);
	void move_physics_layer(int p_from_index, int p_to_pos);
	void remove_physics_layer(int p_index);
	void set_physics_layer_collision_layer(int p_layer_index, uint32_t p_layer);
	uint32_t get_physics_layer_collision_layer(int p_layer_index) const;
	void set_physics_layer_collision_mask(int p_layer_index, uint32_t p_mask);
	uint32_t get_physics_layer_collision_mask(int p_layer_index) const;
	void set_physics_layer_physics_material(int p_layer_index, Ref<PhysicsMaterial> p_physics_material);
	Ref<PhysicsMaterial> get_physics_layer_physics_material(int p_layer_index) const;
	
	int get_terrain_sets_count() const;
	void add_terrain_set(int p_index = -1);
	void move_terrain_set(int p_from_index, int p_to_pos);
	void remove_terrain_set(int p_index);
	void set_terrain_set_mode(int p_terrain_set, TerrainMode p_terrain_mode);
	TerrainMode get_terrain_set_mode(int p_terrain_set) const;
	
	int get_terrains_count(int p_terrain_set) const;
	void add_terrain(int p_terrain_set, int p_index = -1);
	void move_terrain(int p_terrain_set, int p_from_index, int p_to_pos);
	void remove_terrain(int p_terrain_set, int p_index);
	void set_terrain_name(int p_terrain_set, int p_terrain_index, String p_name);
	String get_terrain_name(int p_terrain_set, int p_terrain_index) const;
	void set_terrain_color(int p_terrain_set, int p_terrain_index, Color p_color);
	Color get_terrain_color(int p_terrain_set, int p_terrain_index) const;
	bool is_valid_terrain_peering_bit_for_mode(TileSet::TerrainMode p_terrain_mode, TileSet::CellNeighbor p_peering_bit) const;
	bool is_valid_terrain_peering_bit(int p_terrain_set, TileSet::CellNeighbor p_peering_bit) const;