My reasons aren't measured in pain. More in irritation. On a stock Bontrager saddle (stock equipment) I can ride 30 miles pain free but after the ride I experience an irritaion asi f I am about to develope a saddle sore.
On a good saddle, I still experience some sort of discomfort along the way, I mean it's a 100 miles! A good saddle makes it possible to get comfy on the saddle even after 70 miles where as the lesser saddle, I'd be too irritated to once again achieve comfort.