### 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)
GDCLASS(TileSet, Resource);
#ifndef DISABLE_DEPRECATED
private:
	struct CompatibilityShapeData {
		Vector2i autotile_coords;
		bool one_way;
		float one_way_margin;
		Ref<Shape2D> shape;
		Transform2D transform;
	};
	struct CompatibilityTileData {
		String name;
		Ref<Texture2D> texture;
		Vector2 tex_offset;
		Ref<Material> material;
		Rect2 region;
		int tile_mode = 0;
		Color modulate = Color(1, 1, 1);
		
		int autotile_bitmask_mode = 0;
		Vector2 autotile_icon_coordinate;
		Size2i autotile_tile_size = Size2i(16, 16);