One of the ways to fix this is to add an invisible sprite ShipBase. This will be the object that player will be controlling, so move Drag&Drop behavior to ShipBase sprite. Also move the "Bound to layout" behavior to ShipBase. Set ship position to ShipBase on every tick.
When you attach other parts to the ship, adjust ShipBase size accordingly, so it would always cover the entire ship.
If your ship is irregular shape (not rectangular) and it can rotate, then the above method will not work. In this case it may be easier to add several frames/animations to the ship sprite for different ship configurations. For example, first frame for ship with no attachments, another frame for the ship with attached weapons, another frame for the ship with attached engine, another frame for both weapons+engine attached. The image in all frames can be the same, but the size of the frame and collision polygon will be different.
Here is an example: