The rule is not black and white that you strictly can not call DPI on a fake punt pass.
The rule states (From the LJS article) "Indeed, the NCAA’s rule says defensive pass interference is not to be called when, “there is contact by a (receiving team) player that otherwise would be pass interference during a down in which a (kicking team) potential kicker, from a scrimmage kick formation, simulates a scrimmage kick by throwing the ball high and deep.”
There is room for interpretation from the officials in this rule.
The rule says that the kicker can throw the ball but it must NOT be "high and deep" if DPI is to be called. The HIGH and DEEP part is what is open to interpretation. Not the Punter throwing the ball. The thrown pass must meet BOTH of those requirements in order to NOT be DPI.
The refs (with the help of Brohm I suspect) interpreted that the ball did not meet the "HIGH" requirement of that rule. This is evidenced by the quote from Riley that the refs said the ball was NOT thrown high enough or "arcing" and therefore did not simulate a punt.
This rule should be changed to take the interpretation out of it. It should just state ANY pass from the punter in the punt formation can not have DPI called. And not because of this particular call. High and Deep should be defined. And I bet you would get varying opinions on what constitutes both High and Deep. And once you've defined High and Deep that can be accurately determined by the referee in the field of play the second question you must ask is can a punter from 12 yds behind the line of scrimmage REALISTICALLY meet the requirements of High and Deep? I doubt it.
It is a poorly worded rule that would be interpreted differently by different officials and these officials had the help of the Brohm and the home field crowd to assist in their interpretation.
this also doesn't account for the possibility of the punter shanking it.