Anyone with good enough skills in the studio can make any amp sound amazing. As much as I love a lot of the recorded tones I hear on cd's, I try to see what the live tone is like and base my search for gear on that.
It's all 6505's and Jacksons loaded with 59's and JB's. Simple yet effective.
I actually think the guitars were recorded to sound very organic on Flesh. Minimal multitracking with clear and articulate gain.