Don't know really. It was obviously written with only BTC conversion in mind, not convert to LTC or ETH for example. The reserve balance system will help cope with any transaction fees. Question is, does setting the auto exchange config variable effect any of the payout in other coins code?

EDIT: And of course, you can mine any coin and get paid out in another coin, so never really understood the 'solo mined coins' support on zpools main page.