Well, the raft style at least gives you the opportunity to bounce of the obstacle before it is right under your arse. There is several spots on the Queets we've purposely seen how the two styles of boats (Watermaster and Pontoon) would act in that situation (taking into consideration every situation has many variables coming at you QUICKLY) and we could not get the Watermaster to stick on the rock...it glanced one way or the other. But, I wan't operating the pontoon and don't ever get in one anymore since I have the other rig.
I'll agree that in heavier situations the longer pontoons would serve you better, but tailor your purchase to what you'll be fishing the most and go from there. There was an Abel Travelcraft on the virtual flyshop, brand new, for around $700 bucks the other day. Regular price is $1300. I also know of a new Watermaster Kodiak (the 8foot boat with BIG tubes and large carrying capacity with motor mount, upgraded Carlises, all the bells and whistles that is being sold at dealer cost). Email me if you want the phone # for the shop.