### 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)
undo_redo->add_undo_method(base_control, "queue_redraw");
						undo_redo->commit_action(false);
						emit_signal(SNAME("polygons_changed"));
					} else {
						
						drag_type = DRAG_TYPE_CREATE_POINT;
					}
				} else if (tools_button_group->get_pressed_button() == button_edit) {
					
					int closest_polygon;
					int closest_point;
					_grab_polygon_point(mb->get_position(), xform, closest_polygon, closest_point);
					if (closest_polygon >= 0) {
						drag_type = DRAG_TYPE_DRAG_POINT;
						drag_polygon_index = closest_polygon;
						drag_point_index = closest_point;
						drag_old_polygon = polygons[drag_polygon_index];
					} else {
						
						Vector2 point_to_create;
						_grab_polygon_segment_point(mb->get_position(), xform, closest_polygon, closest_point, point_to_create);
						if (closest_polygon >= 0) {
							polygons[closest_polygon].insert(closest_point + 1, point_to_create);
							drag_type = DRAG_TYPE_DRAG_POINT;
							drag_polygon_index = closest_polygon;
							drag_point_index = closest_point + 1;
							drag_old_polygon = polygons[closest_polygon];
						}
					}
				} else if (tools_button_group->get_pressed_button() == button_delete) {