This is strictly an opinion, because I know nothing about the aluminum shafts and I don't have one or know anyone that uses one.
With that said, stainless has its own issues. Think about what happens to an outboard when a stainless prop meets stump ... no give, resulting clunking noise, trip to dealer, serious reduction in checking account. Stainless sure has the durability edge but not the flexibility. I don't know how many times I've cringed when I got too close to a rock or ledge and watched the whole shaft and control head strain against the bolts holding it on I don't ever try to use my trolling motor like a 4x4, but that flexible mounting system actually sounds like a pretty good idea to me.
Now on the other hand, it could just be a trick to reduce costs. Wonder why they wouldn't make a stainless shaft with a fexible mount?
....BillH