Adam, I see your point about the mountain bike comparison, however, my soft tail bike is like riding a hardtail bike, uphill. Giant used a one way valve that prevents the shock from being pulled around by torque on the chain... I'm not really sure exactly how it works, but it is like riding a hardtail as long as you sit on the seat. The shock looks like it has an oil reservoir, but it's actually the crazy valve.
If you stand up and pedal, the shock's valving is negated because your body movements are pretty big and bob the suspension anyway. My point though, is that would a soft tail still bob if it had a shaft drive instead of a chain?
While I'd have to agree with Setheron, but perhaps there would be a milage difference but nothing we could measure because of the fact that energy is conserved in the springs and the only "lost" forward energy is shed as heat in the shocks themselves.