Great point on the second row of knobs. I think I might have initially been caught in a "emporer's new clothes" mindset, in which I felt a bit ignorant for not being able to get any useful sounds out of those additional modulation controls, and thus too embarrased to express my thoughts publicly. But upon reflection–and after reading your post–I realize that I too found those knobs completely useless.
So I agree 100% with John. Those secondary knobs would be far more useful as additional parameter and filter controls for the algorithms.