As Others have said, its one of those odd things. Like everything else in the game the results of mustering out are subject to GM rule. If you personaly are not happy then put a line through it and write ship share in biro next to it in your rule book. :twisted:
One of the main points of traveller (to me) is the traveling. There are loads of sci fi games around that don't move planets. A Ships boat may be a load of cash (but who wants to buy it) or it starts adventurers visiting the orbital stations and near planets and maybe to that wreck several of them seem to know about. Or as has been said, don't make it a boat, it can be anything which suits the characters background. Was he a merc, a de weaponed light fighter, a medic with an old ambulance, a water submarine, a planetary grav hauler, a short range fuel skiff etc etc.
I tend to be more flexible than the rules say in starting a group, several times I have run multi ship games and been in such games as a player.
What people start with or get later is up to the GM so do what is fun for your players, If your players roll a boat and want to sell it then ask them why they IC don't retire, I would with a few megacredits in a high return account
Or instead of an actual boat leave it as a sort of IOU, you save someones family from death in back story and he owes you big time but cannot repay you then. Later when you want that new jump engine he just happens to run a starport and can get you one for next to nothing but this clears the debt.
I have run two games where players started with boats from mustering.
In one the player had rolled one but I told him he would not start with it, Instead I gave him details on the boat he was co pilot of as a short hauler frieght mover and smuggler in his last term.
later when he was running to join the rest of the group before they jumped out system he, erm, stole it as he had the access codes and I made it easy. It was later used to distract some rather nasty hostiles and blown up.
The other was a moduler cutter sans module and very beat up (lots of negatives) This eventualy would lead to its mother ship which was a merc cruiser in worse state. The players sold everything to refit the merc cruiser and the campaign became merc based.