I can confirm for you, ACC refs are terrible, LOL. I did not closely watch either of your games closely, but I would say that I doubt it's any "welcome to the conference" screw job. I don't think that's the way the ACC does things. More likely general incompetence.
Holding in particular has been a bone of contention for ACC refs for years. Someone broke down a multi-year count of holding calls drawn by each defensive line in the conference. According to ACC refs, FSU's defensive line, with all the draft picks they've had over the years, was the least held team by offensive lines. Duke's fearsome defensive line drew way more holding calls against it over the years. That defies all logic.
Traditionally, if there has been a "bias" in the officiating in the ACC it's been pretty clearly toward parity, rather than toward the favored team. So when you say it wouldn't be surprising for the ACC to protect it's national title contender in Clemson, you are right in general. In every other conference, the team trying to spring the upset gets the bogus call. I don't even think it's "protecting" so much as when you have a questionable bang-bang play, you usually tend to give the benefit of the doubt to the 5-star All-american making the play over the 2-star nobody. Just the way it works (including ACC basketball). For some reason, in ACC football, the benefit of the doubt ALWAYS went against the favorite.
But in the ACC that's a VERY surprising development. In one of our many infamous losses to Wake Forest, it was insane, including a ref re-spotting the ball a foot forward on a Wake fourth down play to give them the first.
What has traditionally happened in the ACC, is you get a team like VT or Miami or FSU with a defensive line full of studs, and they match up against a Wake or a Duke or a Maryland, and they just cannot be legally blocked by the talent on the offensive line. The refs simply swallow the whistle on holding rather than let a team rack up 10+ sacks. Which is exasperating if you are the team getting held on every play, because at least the other team should be forced to bring in another tight end or a fullback to help or something. It also hurts in recruiting stud pass rushers.
Now, what you are describing is kind of in the opposite direction. So to me it sounds like general referee suckitude. Maybe they're moving away from that "refereeing parity" mindset, and just sucking equally for everyone. Or maybe they are moving more toward protecting favorites. But no doubt they suck.