The reason for the loophole:
There was a study done by the Accreditation board of University Aviation Programs.
It profiled a major airline and compared those who graduated from *ACCREDITED* University aviation programs vs. non-accredited, private 61 flight schools, and the pilot factories, (gulfstream, DCA, etc.)
It showed that the job performance and success at the major airline level showed a high correlation between which type of training you received. At the top, Accredited programs. At the bottom, Pilot mills. Can't read too much into it, because it needs to be replicated.
In addition, both pilots in the 3407 crash were from the pilot mills. I think the university loophole is more a way to discourage the fast track, instead of promoting the schools.
Yes it's only one study, but so far it is convincing evidence that success is correlated to graduating from an accredited program.