I'm not an optics engineer, but the vast majority of lenses in any system- telescope, camera, imaging, etc, are all round. That naturally suggests having a round scope tube. Using round lenses in a square tube would just be a waste.
I think squared-off integral mounts on the bottom of scopes would be great, though. For example, if the bottom of the tube had a squared off surface with pairs of 10-32 holes every few inches, a slim base could be screwed on from the bottom, and then clamped to the receiver rail. This is one thing I really like about the ACOGs.
Also note that it's not uncommon for scope reticles to be out of square with respect to the turrets and possibly even adjustments.
In the scheme of things, the flexbility you get by having a plain round tube as the mounting surface is probably more than the trouble to level a scope's reticle, which is pretty easy.
-z