Well you're missing the other huge difference -- that there are two byes in Hockey East and none in the other leagues. I don't know the precise rationale, but perhaps the league didn't want its 3-6 teams to have potentially three more games the weekend before the semifinals. Now the ECAC men do this now for their first round leading up to quarterfinals, but that's a rarity in college hockey history -- the ECAC used to have a single game for a 7-10, 8-9 round. Most leagues have done single elimination for bye rounds throughout history.
I expect that if Hockey East goes to 2 of 3, then they'll do it while expanding the playoffs to 8 teams. I think it made sense back when any given year they had 2 pretty awful teams. Now this season you had a half-decent team UNH and a competitive Vermont team miss the playoffs. I think it's likely they'll expand to an 8 team best of 3 quarterfinal format like everyone else sometime soon. That's pure speculation, I have no inside knowledge of this -- but I think Hockey East's timing in gradually expanding their playoffs has been fairly predictable.