Actually, it only DOES apply to quest characters.Moreover, that would presumably only happen to random officers, not to quest characters. You do not want a storyline derailed because a key character decided to leave you without the story requiring it! So those lines should never be significant in storyline character definitions.
It is specifically intended for the opposite reason that you suggest:
So that if they DO leave because they're unhappy, you'll be able to rehire them in their "homelocation" and finish their quest anyway.
Nice idea, but since it is virtually impossible for it to happen anyway, it is pretty much completely meaningless.