I don't think ND can force any ACC team to play their home games at neutral sites. Those are ACC home games, and ND has to play them by agreement. If VT wants to move our game to FedEx then that is our decision (and I assume ND would have to agree, too). I can't find anything that confirms that part of the agreement, but I also wasn't able to find anything that says that ND can do force us to move our home games to anywhere.
I assume that would mean moving a game like ND/UNC to say Chicago or New Orleans, to reach ND fans, not to Charlotte, where it would be just give UNC another home-ish game. That sounds great to me.
I believe you are right that it is up to the ACC school to decide whether it wants to move its home game or not. The Notre Dame-Syracuse game @ MetLife Stadium appears to be the back half of a home-home series (Syracuse played @ Notre Dame in 2008). It appears that Syracuse made the decision to move the game to a neutral site. Likewise, it appears that Syracuse has decided to move its 2016 game against Notre Dame to MetLife Stadium too. Also, BC decided to move its home game to Fenway. I am pretty sure Notre Dame didn't have any objections to either move. It would not shock me if other ACC schools (including VT) decide to move their home game to a neutral site.