I got the proteus X and the MO Phatt X. That shit is dope. I never had the rack modules so I can't directly compare them sound quality wise, but I would guess that they either sound the same or the software version sounds a little bit better because of the newer soundcard and digital converters. But other than that, they have exactly the same sounds as the hardware versions.
But on another note, the Proteus X is pretty resource hungry, so you need a fast computer to really take advantage of it and play a lot of notes at the same time. But the mo phatt rack guarantees you 64 voices no matter what (and the proteus gives you 128). And also there is the inherent latency thing when dealing with a software plugin versus a hardware rack. The rack module will always have tighter timing.