I assume that a longer seat tube would result in a shorter exposed seat post and a longer top tube possibly in a more forward saddle. This would result in less vertical flex in seatpost and rails and would make an otherwise identical bike less comfortable.
I find what was sometimes called "proportional" geometry problematic on many bigger bikes: Steering angles were steepend and seatangles relaxed to get the longer top tube while maintaining the same wheelbase. This can lead to some awkward handling.
Of course getting your handlebar where you want it is more important than frame angles, and (i like my bars fairly high) would always get the larger frame before resulting to a Nitto flagpole stem to get the bars higher.
Tobit Linke, Dortmund, Germany