### 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)
const real_t circle_radius = circle_shape->get_radius();
				Vector<Vector2> shape_outline;
				int circle_edge_count = 12;
				shape_outline.resize(circle_edge_count);
				const real_t turn_step = Math_TAU / real_t(circle_edge_count);
				for (int i = 0; i < circle_edge_count; i++) {
					shape_outline.write[i] = static_body_xform.xform(Vector2(Math::cos(i * turn_step), Math::sin(i * turn_step)) * circle_radius);
				}
				p_source_geometry_data->add_obstruction_outline(shape_outline);
			}
			ConcavePolygonShape2D *concave_polygon_shape = Object::cast_to<ConcavePolygonShape2D>(*s);
			if (concave_polygon_shape) {
				Vector<Vector2> shape_outline = concave_polygon_shape->get_segments();
				for (int i = 0; i < shape_outline.size(); i++) {
					shape_outline.write[i] = static_body_xform.xform(shape_outline[i]);
				}
				p_source_geometry_data->add_obstruction_outline(shape_outline);
			}
			ConvexPolygonShape2D *convex_polygon_shape = Object::cast_to<ConvexPolygonShape2D>(*s);
			if (convex_polygon_shape) {
				Vector<Vector2> shape_outline = convex_polygon_shape->get_points();
				for (int i = 0; i < shape_outline.size(); i++) {
					shape_outline.write[i] = static_body_xform.xform(shape_outline[i]);
				}
				p_source_geometry_data->add_obstruction_outline(shape_outline);
			}
		}
	}
}
void NavMeshGenerator2D::generator_parse_tilemap_node(const Ref<NavigationPolygon> &p_navigation_mesh, Ref<NavigationMeshSourceGeometryData2D> p_source_geometry_data, Node *p_node) {