Stock for the V6 is only 60mm. They're 65mm for the V8. That's for 99+ (new body style). The 94-98 V6 TBs were - get this - 50mm(!!!!!). Talk about strangling airflow...no wonder the 94-98 V6s only made 140hp. You can get aftermarkets, like BBK, in just about any size you could want, though. 70mm, 75mm, whatever.
Actually it's funny you mention that, I was going to say something about boost before.

If you were running high boost, I might be inclined to leave the shaft alone. Or at least take it VERY easy on the 'meat removal' part. If you've ground the shit out of your shaft, then try to run 20 pounds of boost with it, it wouldn't surprise me at all to see the shaft twisted and snapped. You could help prevent that by making sure you have good pressure-release hardware upstream from the TB.
To be honest, though, I think I agree with you. I don't know if I'd mess with the shaft at all under that much boost. When you're boosting, smooth airflow isn't as critical as it is NA, so I'd probably be more inclined to just go with a bigger TB (if you even need it), and not waste time haftshafting.
If you're talking about the integrity of the actual aluminum body itself...I highly doubt that'd be an issue. You'd punch through a gasket way before you blew a hole through aluminum.