It's intentionally a balancing mechanic, so if you have fewer players, they get more skills each than if you have more players. It makes sure, among the whole crew, you have enough of the basic skills that you don't end up in a space trader campaign where nobody actually knows how to dock a spaceship.

For a new player, that's up to the table to decide. As Sakul_Aubaris suggested, as each skill package has 8 skills, then giving that player 8/(number of players) skills (maybe from the same package the players originally picked from) could work. You could also "handover" the package skills the departing player had. Or the referee and the players could agree on any other sort of arrangement that makes sense. You could decide that, given that the other players have a lot more skills by this point, there's no need for a skill package, and the new player is just going to be less experienced than the veterans, or you could decide to add additional bonus skills to help the new player catch up. It all depends on how you want to approach it at your table.