### 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_do_method(base_control, "queue_redraw");
						undo_redo->add_undo_method(base_control, "queue_redraw");
						undo_redo->commit_action(false);
						emit_signal(SNAME("polygons_changed"));
					} else {
						drag_type = DRAG_TYPE_PAN;
						drag_last_pos = mb->get_position();
					}
				} else {
					drag_type = DRAG_TYPE_PAN;
					drag_last_pos = mb->get_position();
				}
			} else {
				drag_type = DRAG_TYPE_NONE;
			}
		} else if (mb->get_button_index() == MouseButton::MIDDLE) {
			if (mb->is_pressed()) {
				drag_type = DRAG_TYPE_PAN;
				drag_last_pos = mb->get_position();
			} else {
				drag_type = DRAG_TYPE_NONE;
			}
		}
	}
	base_control->queue_redraw();
	if (!use_undo_redo) {
		memdelete(undo_redo);
	}
}
void GenericTilePolygonEditor::_set_snap_option(int p_index) {