And what would the reasons for a waiver be?
When the STUDENT athlete is oh so close to qualifying in one of the eligibility areas, usually core course requirements, and has a little orphan annie tale of woe, backed by stochastic studies of predicted academic success, the NCAA might relax the standard, allowing for some participation. However, those who follow such things know that such waivers aren't granted except in extraordinary circumstances, like don't bother asking if you expect full participation, ie practice, competition and $'s.
As for reconciling the BE's policy of not allowing nonq's, yet allowing the member institution to request relief from the eligibility criteria, look at it like this: the athlete, once granted the waiver, is deemed to have qualified to the extent outlined in the waiver, so in the BE's eyes, the athlete is no longer nonqualified. I personally think that this policy is reductio ad absurdumemmertisapussyhypocrite.