ArtCo would cry if I said yes to player made whalebone-esque ships
For user content, you can (in theory) make up a ship from scratch, provided that it follows the normal sort of ship design styles of the period. No crazy bonkers unique ships would be allowed.
If you're thinking of that route though, I'd strongly advise a very slow initial pace, so that the 3DSC can properly advise you on how the ship is looking early on when it's easy to make adjustments
