### 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 remove_layer(int p_layer);
	void set_layer_name(int p_layer, String p_name);
	String get_layer_name(int p_layer) const;
	void set_layer_enabled(int p_layer, bool p_visible);
	bool is_layer_enabled(int p_layer) const;
	void set_layer_modulate(int p_layer, Color p_modulate);
	Color get_layer_modulate(int p_layer) const;
	void set_layer_y_sort_enabled(int p_layer, bool p_enabled);
	bool is_layer_y_sort_enabled(int p_layer) const;
	void set_layer_y_sort_origin(int p_layer, int p_y_sort_origin);
	int get_layer_y_sort_origin(int p_layer) const;
	void set_layer_z_index(int p_layer, int p_z_index);
	int get_layer_z_index(int p_layer) const;
	void set_layer_navigation_enabled(int p_layer, bool p_enabled);
	bool is_layer_navigation_enabled(int p_layer) const;
	void set_layer_navigation_map(int p_layer, RID p_map);
	RID get_layer_navigation_map(int p_layer) const;
	void set_selected_layer(int p_layer_id); 
	int get_selected_layer() const;
	void set_collision_animatable(bool p_enabled);
	bool is_collision_animatable() const;
	
	void set_collision_visibility_mode(VisibilityMode p_show_collision);
	VisibilityMode get_collision_visibility_mode();
	void set_navigation_visibility_mode(VisibilityMode p_show_navigation);
	VisibilityMode get_navigation_visibility_mode();
	
	void set_cell(int p_layer, const Vector2i &p_coords, int p_source_id = TileSet::INVALID_SOURCE, const Vector2i p_atlas_coords = TileSetSource::INVALID_ATLAS_COORDS, int p_alternative_tile = 0);
	void erase_cell(int p_layer, const Vector2i &p_coords);
	int get_cell_source_id(int p_layer, const Vector2i &p_coords, bool p_use_proxies = false) const;