Reviewing a proposal on a 412(i) plan (not prepared by us) and it appears that the salary figures used in the proposal were based on compensation excluding bonuses rather than total compensation. Is it allowed in a 412(i) plan to use a non-safe harbor definition of compensation? Obviously this lowers costs for everyone but the owners (who are both well over 200k).

Yes, it's allowable. But if discriminatory, obviously it won't fly.