I read the full article and came away with the following impressions:
1) Nebraska is 'meeting' Title IX requirements within what appears to be a realm of acceptability, but whether or not it would fully stand up in an arduous Title IX investigation is unclear.
2) To further qualify point one, it's unclear whether Nebraska (or, really, any number of schools) would stand up to an arduous Title IX investigation because investigations are mostly the result of a complaint/whistleblower system. Right now, nobody is really complaining at NU, and one of the swimmer walk-ons they quoted said they loved the experience.
3) It can be difficult (though not impossible) to prove roster padding. You'd essentially have to prove the rosters being padded are being done so at an uncommon rate compared to similar programs across the country. You'd also have to prove that the players being padded are of unequal value (in this case, to their football counterparts) and thus taking away opportunities from more deserving (in this case, female) athletes.
The one quote in this article that seems to explain the situation best is from Moos when he said they're the "uppermost diligent on compliance as we see it." They're probably not complying with Title IX to the exact letter of the law. But, they're also probably close enough to avoid provable Title IX violations. They're massaging the system like a lot of places would.