Basically we do 4-5 takes of every part and then pick the best one. The way we work with Jens has always been very musical, and that's the way I write too. If we can't play it we won't use it. To be honest I've never ever given up on a riff or a part because I or we haven't been able to perform it.
Same with autotuners, if I wouldn't be able to sing I'd be terribly uncomfortable with having a machine have me sounding like I could. We do many takes and pick the best ones. What Jens does later I don't really know, but I can easily hear a autotuned part I believe and I'm allergic to them. But with that said I'm sure we've used it here and there, especially to "tighten" together multi tracked harmonies if they're too chorus-y sounding.
Nowadays I don't track my vocals very often, like I did on say "Still life". Now we pick a single take of a single line so it'd better be good.
Recording albums these days is ridiciously time-consuming and the technical devices out there are mind boggling, but Opeth have always taken pride in being a band who actually can play and perform everything we put on tape. There's nothing fake about us, I can tell you that, but sometimes we dive into the new technology as everyone else.