If you want to be eligible for the D1-A tourney, you must commit at the first of the year that you will play in the D1-A tourney if selected. As I understand it that means if one of them got selected for the D1-A tourney and they were supposed to play in the Varsity Cup at the same time, they would have to forfeit the Varsity Cup. Either that, or maybe they could send their A-side to one match and their B-side to the other.
Either way, the majority of VC teams don't bother with it and just rule themselves ineligible. The financial incentives are better in the VC and the overall level of competition is, as well. Consider -- Air Force got eliminated in the first round of the VC, yet here they are getting a bye into the Quarter-finals of the D1-A tourney.