First, Miami is in the ACC and made the playoff.
Second, it makes more sense to take the 12 best teams in football. If we want to have a subjective committee or design a computer ranking, that's a stylistic choice, but guaranteeing a G5 team a spot doesn't make a ton of sense, especially in many years when it is likely there will be a well-rested Big Ten or SEC team sitting at number 5.
Third, ND has nobody to blame but themselves for losing to Miami and A&M. They also have nobody to blame but themselves for their arrangement with the ACC. I think there are plenty of walkover teams in the middle and bottoms of all conferences, but ND's ACC arrangement has aged poorly, especially with Clemson and Florida State backsliding and no guarantee for the league to give ND teams at the top of the league.
The NBC deal is worth to Notre Dame about what each Big Ten team takes from the league's media rights.