I am guessing Andrew is talking about a situation like this:
That looks like a tossup as to which way the b-string should go. And I don't think the nut, tuner, or neck/headstock structure would be effected either way. It would be very unusual to have that key be the only reverse direction tuner but I bet nobody would notice unless they tried to tune it for you. It could be your secret tweak!
Also, as Adriaan said, you don't need many windings to keep the string in place. My way is to start with the tuner's slot going the same direction as the neck, then I wind the string around 1 time, bend it down through the slot and then bend it outward. So I am only starting with 1-1/4 turns of string in contact with the tuner. I've never had a problem with slippage...
Jimmy J