### 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)
color = NavigationServer2D::get_singleton()->get_debug_navigation_geometry_face_color();
#endif 
		if (p_selected) {
			Color grid_color = EDITOR_GET("editors/tiles_editor/grid_color");
			Color selection_color = Color().from_hsv(Math::fposmod(grid_color.get_h() + 0.5, 1.0), grid_color.get_s(), grid_color.get_v(), 1.0);
			selection_color.a = 0.7;
			color = selection_color;
		}
		RandomPCG rand;
		for (int i = 0; i < nav_polygon->get_polygon_count(); i++) {
			
			Vector<int> polygon = nav_polygon->get_polygon(i);
			Vector<Vector2> vertices;
			vertices.resize(polygon.size());
			for (int j = 0; j < polygon.size(); j++) {
				ERR_FAIL_INDEX(polygon[j], verts.size());
				vertices.write[j] = verts[polygon[j]];
			}
			
			Color random_variation_color;
			random_variation_color.set_hsv(color.get_h() + rand.random(-1.0, 1.0) * 0.05, color.get_s(), color.get_v() + rand.random(-1.0, 1.0) * 0.1);
			random_variation_color.a = color.a;
			Vector<Color> colors;
			colors.push_back(random_variation_color);
			RenderingServer::get_singleton()->canvas_item_add_polygon(p_canvas_item->get_canvas_item(), vertices, colors);
		}
	}
	RenderingServer::get_singleton()->canvas_item_add_set_transform(p_canvas_item->get_canvas_item(), Transform2D());
}