Bowl payouts are net of ticket sales requirements. If the payout is $10 and the team sells only $1 of its $2 allotment, then the payout to the team is $9.
And if it's going to cost the school $10 to get the team, including support staff, cheerleaders, etc to & from the bowl and put them up in a hotel and feed them, then the school is losing $1.
Schools often (perhaps usually) lose money on bowl games.
It's not about how many FCS teams you play, it's about how many wins over FCS can count towards bowl eligibility. That number is 1. You can play more than one FCS school, but you're essentially making it more difficult for your team to be bowl-eligible because only one of the (expected) two wins matter in the quest for a bowl.
I think the "pass" (waiver) you're thinking about for Army was for the 2015 game against Yale to count towards bowl eligibility. The game against Yale - a non-scholarship FCS school - was played at the Yale Bowl as part of the 100th anniversary of the stadium, so the waiver request was grounded in the historical nature of the game. Note that the waiver wasn't even used because we lost to Yale (and didn't come close to bowl eligibility).