### 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)
ERR_FAIL_COND(!tile_set.is_valid());
	
	Vector2i hovered_coords = TileSetSource::INVALID_ATLAS_COORDS;
	int hovered_alternative = TileSetSource::INVALID_TILE_ALTERNATIVE;
	if (drag_type == DRAG_TYPE_NONE) {
		Vector2i mouse_pos = p_transform.affine_inverse().xform(p_canvas_item->get_local_mouse_position());
		Vector3i hovered = p_tile_atlas_view->get_alternative_tile_at_pos(mouse_pos);
		hovered_coords = Vector2i(hovered.x, hovered.y);
		hovered_alternative = hovered.z;
		if (hovered_coords != TileSetSource::INVALID_ATLAS_COORDS) {
			TileData *tile_data = p_tile_set_atlas_source->get_tile_data(hovered_coords, hovered_alternative);
			int terrain_set = tile_data->get_terrain_set();
			Rect2i texture_region = p_tile_atlas_view->get_alternative_tile_rect(hovered_coords, hovered_alternative);
			Vector2i position = texture_region.get_center() + tile_data->get_texture_origin();
			if (terrain_set == int(dummy_object->get("terrain_set"))) {
				
				Transform2D xform;
				xform.set_origin(position);
				Vector<Color> color;