The other thing - he was using Mainstage for effects you can't get with rackmount or pedals, sort of el-specializo digital type fx.
I'm not 100% convinced on the AxeFX thing either but it can produce decent sounds. I know Bill Ruppert sold his and got another VG-99 so that says something.
I think the biggest problem is that for Clockwork Angels the guitars got tuned lower and lower to accommodate Ged's changing voice and guitars just don't ring well at those uber low tunings - they're great for the "chunk/djent" thing. But it's hard to get an idealized tone in a live environment.
And a live tone with a ton of reverbs and delays and choruses ends up sort of diluting the tone a bit.
Also, the Lerxst amps were supposed to be modern replicas of the Marshall Silver Jubilee amp that he rented and liked - he didn't get those amps until day one of the
tour - I wonder how many days he had the amp when that stuff was recorded? I still think the Mesa Mark V probably would have given him a better distorted lead and/or
rhythm tone.
I've heard some reports that he was going back to PRS guitars in the future but who knows.