This occurred to me years ago when first playing the game, but I only just remembered now:
Do you think the W-Y FTL Ship is intended to be a retconned redesign of the Patna from Alien 3 (which would mean it is also named Patna, actually)? Wouldn't make much sense, in-universe, for Michael Bishop to switch ships after carting the Conestoga class all the way to FIORINA 161.
Considering there are already two Conestoga class in the game, I can understand the desire to get a bit more variety and differentiation into the mix as well.