The reason is two-fold: It helps smooth out the payments to the conferences which allows better financial planning. No conference gets a financial windfall just because they have two domininant teams that appear in BCS games multiple years in a row.
I don't remember the exact payout, but yes ND agreed to a lower payout for an appearance with a guaranteed annual payout. Given the current trajectory of ND, this was a very good deal for the BCS conferences.
Simply because anti-trust laws keep a monopoly from imposing itself. What I don't get is all this silly harping about ND. They really aren't being treated any differently than a BCS team and it's ridiculous to claim they aren't worthy to be treated as such. Yes they get an automatic if they are ranked 8th or higher. LSU got an automatic being ranked 13th in 2001. Where were all the peasants and their pitchforks then? Yes they get annual guarantees of payments, but so does every other BCS team. The bowls like them because they put a lot of butts in the seats and bring good ratings. Being in a conference will not change that or bitching.