The performance BYU's defense turned in against Baylor was comparable to the defensive "performance" of Kansas earlier this year. Even worse, elements of the defense (such as rushing techniques and blitz packages) clearly lack sophistication.
I think you hit the nail on the head when you mentioned Tuiaki's successes last year - he's clearly capable of solid performances against Sunbelt-level teams when he has the more talented roster. Is he capable of stopping a traditionally middle-of-the-road Big XII team from having a field day? That's the question that will need to be answered as BYU transitions from independence to a P5 conference. BYU is almost always going to be at a talent disadvantage against P5 schools and relies on coaching to bridge the gap - so the basic schemes and unsophisticated techniques we're seeing from Tuiaki are particularly concerning.
Tuiaki was very gracious with me in our personal interactions (when he was early in his career at Utah State) and I don't personally wish him anything but success. But it's very possible that a guy can be honorable and good and still be out of his depth in a particular career position. We're in the 6th year of Tuiaki's defense; he should have "his" guys and should now be solidly responsible for his unit's depth, development, and technique. The competition is about to get much stiffer, and I think that BYU fans are justified if they have concerns about whether Tuiaki will be equal to the challenge.