I've contemplated this myself...there some good thoughts in the thread. Next time I do a 2 hr session, I'll try taking my front wheel up a bit. I normally have my bike level (and yes, I wear cycling shorts every time).
My trainer sessions are very constant effort (sometimes heavy effort, sometimes light) but constant nonetheless. I look at my ride logs and they are anything but. Uphill, downhill, coasting, stopping, off the saddle, on the saddle...my rides are very dynamic. My trainer sessions, even if I get off the saddle every 10-20 min for 30sec at a time...very constant effort. That's the reason why I cap my sessions at 2 hrs, my effort is greater than on the road.
Such is the nature of the beast I guess, I've kind of come to accept that being temporarily saddle sore comes with the territory during trainer sessions.