It doesn't matter what you set your exchange as. I send all my auction orders to SMART (with OPG or MOC defined) and they all are automatically routed to the native exchange. EDIT: It doesn't matter whether you set the exchange to native or SMART. It should matter if you have an arca name, want to participate in the nasdaq auction for it and then set nasdaq as exchange.
I assume the broker does not get payment for order flow, when the order is a marken-on-open or market-on-close auction order. However, I do not think IB or Schwab for instance can accept MOC and MOO orders and not let these orders participate in the auctions. At least they have to inform customers clearly that the orders will not participate in the auctions. Since Schwab offer these order types and customers do not pay commission, I assume those orders are clear cut auction orders without commission and without payment for order flow.