No. If it was per "encounter" then if the encountering player attempted both combat checks they couldn't use a weapon for both checks. Same thing for someone wanting to attempt both combat checks and play 2 attack spells. That would stink. That is why it is per step of the encounter, and the two checks to defeat a villain are two different steps of the encounter.
In large groups, I've found that the villain usually isn't the greatest challenge, though its still possible to be caught unprepared by a surprise encounter. The bigger obstacle is "can you get setup to beat the villain in time?"
FYI: Through the end of Hook Mountain Massacre (so 18 scenarios) I believe 17 banes required 2 checks to defeat. Though not all are villains.
The "final battle" kind of boils down to whether the villain takes you by surprise or if you have the ability to scout it out and plan your attack. My last game, we had to defeat the Skinshaw Man. We discovered his location early, and then decided to close down 3 of 6 locations (4 players). We spent the end of the game preparing for the battle, by going around the table twice just moving (2 to encounter the villain, and 1 each on the open locations to prevent his escape) and by discarding cards to stock up on blessings and other cards to help in the final battle. Nobody did any explorations.
So when we were ready, my wife encountered the Skinshaw Man, our friends temp. closed the other locations, then she proceeded to do the first combat check. She needed a 15 (due to a Haunt) and rolled something like the high 20's. I did the second check and wound up rolling in the 40's! Because we had time to prepare, everyone contributed at least something to the roll. In the case of our Harsk, he added a blessing, 1d4 for his power, and 1dX for a weapon ability on each roll! No need to hold back if you know this will end the game.
Anticlimactic? Maybe. But I look at it as good adventurers strategizing and going in prepared. Too often when we encounter the villain by surprise, we wind up chasing him all over the board because he escapes or we fail our rolls. While a villain fight on the final turn of the game with a hail mary roll is exciting, it's also really disappointing when you fail it.