The single biggest problem with Notre Dame against Clemson was Wimbush being a miss in recruiting. He was composite top 50 player, borderline five star. Notre Dame had about five possessions against Clemson with a chance to tie or take the lead. It snowballed against their defense, but there was also the realization when it got to 16-3 that the deficit was probably too much. Ian was limited in how he could hurt Clemson; didn't have the legs to scramble, didn't have the arm to hit them over the top. Brandon had that skill set, but not the consistency. You get good Brandon out there, Notre Dame can compete with them.
But, I said compete. As in 3-4 out of 10 times they can win if the breaks favor them. As you point out, they'd need to get more top line players to be in a situation where they are favored against a team like that. And that's the goal. Don't be competitive, be favored. Clemson came into the game with nine five star players on the roster. Notre Dame had one. There is your difference.