Here's what Leipold said (and what a Jayhawk reporter wrote) after the game:

Early in the fourth quarter, Kansas opted to have Jalon Daniels kick a quick punt after the Jayhawks were in no man’s land on fourth-and-long. The punt hit off the helmet of a BYU player and Quentin Skinner was able to fall on it.

Following the lucky break, the Jayhawks scored the game-winning touchdown. Leipold said they’ve always practiced this, and it worked out in their favor.

“We've done it every Thursday since I've been a head coach, and I think we've done it three times, and two of them have worked out really well, and this was one of them,” Leipold said. “So, it's something that we've worked on. It's something to have just in case. Obviously, we didn't plan on it working the way it played out there, but it was huge. And again, Quentin Skinner, who's on the punt team to begin with, does a great job covering things, was really aware of the situation, landing on the ball.”

Sounds like it was a well executed play that is designed to catch the defense unaware.  Working out really well seems to be pinning the other team deep.  Getting the defense to have to address the surprise punt and have their defense (instead of the return team) deal with the punt means that you have players who usually don't field punts having to deal with the ball.  Whereas Parker Kingston spends time every practice lining up and knowing which balls he will return, which he will fair catch and which he will let go over his head for a touchback, your starting defensive backs don't do that.  So that adds to the chance of something crazy happening. 

So they caught us by surprise, and then I think both Leipold and the reporter acknowledge in their comments that the ball hitting the defender in flight was a lucky, unexpected development (but admittedly among the many unpredictable things that can happen in the chaos of a play like this).