Re: Hendrix' non-play in the last two games. Everyone who is not in the lockerroom, practice field, nor war-room doesn't know what we're talking about, so let's at least start there.
To make some wild and humble guess: A). Andrew Hendrix and his "specialty package" should be looked upon by us, not identically of course but, similarly to trick or gadget plays. Kelly does not view "it" as part of the regular offense.
B). Kelly is primarily interested in winning the game currently being played. He is not primarily interested in preparing for some more distant future. He is, of course, not at all interested in the curiosity of fans or media. As such, he will manage games with immediate winning in mind.
C). All good in-game play-callers must have great instinctive feelings about the instant moment-to-moment nature of the game. They have to "feel" what is likely to work and make that decision in seconds at most. If one "feels" that it's time for a gadget play, one gambles. If one doesn't "feel" the Hendrix Package, then one doesn't put it in.
I used to coach a little basketball. Everytime I found myself restricting my substitutions to some pre-thought-out "mechanical" way of ensuring that people got playing time, the quality of play went downhill. If I could merely "feel" the game, and spontaneously substitute when "right", we played better. If I EVER could have just let certain players sit the bench for entire games, I'd have been in heaven and we'd have won more.
I don't see what Kelly is doing as markedly different. Thankfully he doesn't have to care much about whiny players, parents, and fans. Kelly will play the Hendrix Package when he feels it will help Notre Dame win now, or when the game is well in hand so that it might help Notre Dame win later.