Transfer mod finds everything in player storage and copies it into their fleet in the new save. The way to prevent a ship from being copied like that is to make a special market for it - see the Autofactory for an example of a market with some really strange rules - you'll probably want a -100% tariff (so the player can pick up the ship for free), and rules that prevent the player from selling anything to the market.
(Edit: Or, of course, you could say that the save transfer mod is a form of cheating - which it kinda is - and that you're just not going to worry too much about it.)