Mike, I might be alone on this one and I don't pretend to have any scientific methods or anything backing me up....but here's my reasoning:

I feel like there's a difference in the ride of a smaller frame bike with a long stem versus a bike thats larger with a shorter stem. I like to stretch my upper body out when I ride, and I prefer the feel of a larger frame over a smaller one...so I prefer a long top tube.

You're right that I could take a 58cm frame and with a longer stem make the saddle to bar distance equal to that of a 61cm with a shorter stem. To me the larger frame would feel better, will have a little more give to it, and ya know everything on the frame is a little bigger too so I feel like it changes the ride...at least enough for me to prefer a larger frame.

I don't get concerned over standover height unless my feet don't reach the pedals when the seat is all the way down. I never stand flat footed on the ground with the bike straight up and down underneath me and I have yet to run into an emergency stop situation where I was required to come to a stop and stand in that position. I love my nads as much as any other dude...If I thought riding a big frame was endangering 'em I'd probably ride smaller frames.

like I said though... this is my preference. I don't expect anybody else to feel the same way.