Half a century ago, most "good" bikes had the stem and top bar set as high or higher than the saddle, and the saddle was a firm leather Brooks. And yes, people were sitting on your "sit" bones. High quality bikes of the 1960's were designed for "real" people to tour in comfort, not for pretending to be getting ready for the "Tour de France".
"Marketing" has dictated that most new bikes today, even the ones at Wal-Mart, look like "racing" bikes. So, I often see people cruising to the grocery store, bent over in racing position, their stem three inches lower than their saddle. To deal with the resulting pain, they have a heavily padded seat, with the padding pressing hard on things that are not enjoying the ride.
I have set up most of my bikes so that my hands will be higher than the saddle. I use fairly wide, but firm Specialized Body Geometry saddle. The BG saddle puts firm support under my sit bones, and open air under the stuff that I don't want to sit on. The combination of having my hands higher than my saddle, and a wider, firmer saddle has allowed me to be comfortable on both long and short rides.
And, the bonus of the higher hand position is the elimination of pain or stress on my hands, wrists, arms, and neck. Most of us ought to give up trying to look like Lance, and start enjoying riding in comfort.