Hmm... the reason I did that is when I get a new pilot they are very unskilled, so it is safer for them to gain experiencing piloting the mothership instead of flying a generation 1 or 2 fighter.

It's not a big problem. I think I only did this for 1 or 2 pilots in all the story paths together, it's ok if this doesn't work. Maybe you can just write a warning in the first post of this thread.

Edit:
By the way, thanks for the credits link to StarRover forum, I can see there's been quite a spirited discussion there