Kal,
I saw that the Velo's auto mode didn't utilize the capabilities of the PEq, hence my first comment that my results might be due to issues peculiar to the Velo's auto correct system. However, I'd love to find any auto system that can optimize all of the crossover settings - points (which may be asymmetrical), slopes (which may be asymmetrical), phase, and polarity (not the same). After that, it must adjust for smoothest response through the crosssover point, so that the transition from mains to woofer is seamless. After optimizing this critical transition, it can then determine which trade offs between ideal response through the crossover versus smoothest overall response are optimal. The latter is tricky because the smoothest transition may occur around a crossover point that is either too high or too low to provide natural octave to octave balance throughout the overall bandwidth of the combined system. If this is the case, it must try again.
BTW, if you reverse the process and try to optimize overall bandwidth balance first, there's a good chance you'll try hari-kiri before you get the subs integrated in a satisfying manner.
Such a system may exist - I'm not remotely familiar with what's out there. I'd just personally prefer the option of tweaking manually - especially if separate subs are involved - just in case the auto system comes up short.