Yep, shorter tubes would be stiffer.

It probably has something to do with the fact that Torque=Force x Distance from pivot. So when you're pedaling, you're applying some Force at some angle away from your downtube and chainstays. The resultant torque causes the flex. With shorter tubes, you have a shorter distance from the pivot, and thus a smaller amount of torque is applied to the tubes.

A longer seat post would probably contribute to some flex, but when you're pedaling hard, a lot of your mass is offset by the opposing force from the pedals. So your effective weight on the bike is lower anyway.

I'm just speculating here-- correct if I'm wrong.