Yes, to be fair to Wolf's Head, the magazine article makes it very clear that they ran into problems specifically because they recorded the instruments one at a time, wearing headphones, to a click track. i.e. doing something that didn't play to their strengths.

If you're used to playing live as an ensemble, this can be a very difficult thing to do. I personally find recording while wearing headphones to be very unnatural. You're just not hearing yourself the way you normally do. Pitching's difficult.

With acoustic instruments, and bands whose strength is playing live, there's a lot to be said for just micing the whole ensemble with two good omnidirectional microphones. And maybe hedge your bets with 1 or 2 extra up-close mics for the lead melody instruments.

I still find it rather staggering to hear what a good mixing engineer can do though. There's another "before and after" on that same page of a rock band called Free Radicals. The difference between their original and the remix is almost absurd.