No - I rarely use S mode. I do find myself opening the throttle much more on the CVT than I would do in a manual. You are dead right about cruising speeds though because, at 70, the CVT is well below 3,000 rpm whereas a manual would be at around 3,500.
PS
The low speed figures perhaps shed even more light. The manual EX Navi will record 40.4 mpg at "low speed" as opposed to only 36.2 for the CVT. "Low speed" is the nearest to an urban cycle from what I read.
That's a big difference - over 10% less efficient for the CVT.
I have to say it feels right to me because of the length of time I spend at high revs. In the last manual I had I would change up, in an urban setting, before 2000 rpm. Coming back from the supermarket today I've hit 3000 rpm a couple times just to keep pace with traffic - not indulging in the traffic light Grand Prix just making normal progress.