First, in Wiley's case it's both. Editing & writing rise to the level of fraud, whereas simply typing a paper (or portion like a works cited page) is not always considered to be fraud. It's merely an extra benefit that doesn't necessarily rise to the level of "unethical conduct." The NCAA opted to just allege the Article 10 violations as they (and the associated penalties) were sufficient.
This is not an uncommon practice. The NCAA could have easily hit UNC with a violation of 14.2.2.6 (b) in the most recent NOA. It states independent study courses may be used to maintain eligibility provided:
"The student-athlete enrolls in the course in the same manner as is available to any student;"
Per the NOA itself, that clearly didn't happen. However, the 16.11.2.1 allegation is sufficient to warrant omitting 14.2.2.6(b) from the NOA. Keep in mind that Jan Boxill is also alleged in the NOA to have done the exact same thing as Wiley (writing conclusions of papers), yet academic fraud is never mentioned. There will be differences from one NOA to the next based upon the facts, the stance of the university, and the approach the NCAA believes will work best.
At any rate, regardless of it being labeled fraud or simply an extra benefit, any extra benefit renders an athlete ineligible pending reinstatement proceedings. There is a difference between a "benefit" and an "extra benefit." The NCAA describes benefits (and associated limits) that are permitted. The only restriction is that they be provided to all students, unless the NCAA states an exception. Extra benefits on the other hand, are always an issue and always result in ineligibility until reinstatement occurs.
Athlete specific tutoring is a "benefit" mandated by the NCAA (16.3.1.1). However, what UNC did went beyond the bounds of the described benefit and therefore was determined to be an "extra benefit." This pulls it out of the restitution provision and the athletes are ineligible.
In the cases of the other NOAs, the NCAA is not asking whether those Universities believe the involved athletes were ineligible. That is not the purpose of the request, though I see why you thought that's why I was getting at that. My point was poorly phrased. The purpose of the request is to provide the schools the opportunity to state whether the school believes there are mitigating circumstances that would warrant waiving any vacating of victories. An assumption of ineligibility is implicit.