I guess it depends on how you ride, but I don't apply much lateral force (or fore and aft force for that matter) at the saddle. When in good form I don't even put much weight on the saddle, so I don't see where short seat tube length with a long post is likely to be negatively affecting apparent frame stiffness. The forces that make the frame flex are at the bottom bracket and (especially for standing climbing) at the head tube.

I like my compact frame just fine. I find it comfortable and think that I can tell that it is stiffer at least when loaded touring. I admit that since I don't have two otherwise identical frames I can't be positive whether or not I really can feel the difference.