2-disk was designed for the lower horsepower Yamaha Can. The Yamaha Pipe has more horsepower, obviously. My guess as to why they run the 2-disc is because it is more readily available, or they use it when switching to Can. I would contact your engine builder to get their advice. My guess is horsepower related.
The 2-disk is OK for a jr canned Yamaha. For a Yamaha senior with a pipe, I’d go with a 3-disk, six spring. I know that’s more rotating mass, but I believe that it’s easier to adjust, will hold that adjustment and there will be fewer head aches.