I don't think it's a nightmare, but passive subs with external amps do seem analogous to buying a modern automobile engine and using a generic engine management system, and not the one from the engine manufacturer. The combination might work, but it won't run as well as the dedicated design. I don't even want to know what Velodyne did to get my DD18+ to perform the way it does. I'm guessing I would be appalled if I knew.
Yeah, I get it that you use Audessey to pre-distort the signal for its room correction strategy, but my impression, perhaps incorrect, is that's a blunter instrument than what a sub manufacturer does with a custom amp.