One of my friends who is a pretty successful recording engineer/producer swears by re-amping, there's no doubt it can "dial in" the tones more accurately and it takes away a lot of variables, but it does just feel less like a real recording experience to me haha. I'm a curmudgeon though.
That being said, as for all the talk of presets and everything, there is a 0% chance they would just use a preset and then say "that's that!" You can still tweak tones, EQ, add effects, put it through the entire mixing/mastering process, whatever. It's just the initial sound. A random dude trying out a Mesa Boogie amp isn't going to sound exactly like Enema era Tom either.
I would prefer to hear that they were using some kind of dope vintage amps and cabs and going for these awesome tones and blah blah blah, but when it comes down to it we probably wouldn't be able to tell much of a difference anyway. With the current state of this type of technology, if they want a certain tone, they'll be able to find it.
Based on what Mark's bass tech has posted on Reddit, they are modeling the bass settings directly after Jerry Finn's actual amps, literally, and it comes up with an almost exact replication of the tones they have used in the past. If they're going that far for the live show, I'm sure they're doing something similar in the studio.