I was concerned as well, but if Vai can have it done to his Jem, so can I. I have the same guitar. He moved the nut towards the bridge about an 8th of an inch. My Jem is a 98 so it has the older locking nut that's screwed in from the back of the neck. So he had to fill the holes on the back and re-drill them. On a scale of 1-10, I would say it's a 7 as far as looks goes. You can see the glue, but it doesn't look bad. It's on the back of the neck anyway. From the front, you can't really tell the difference. I told the guy that I was a NUT about the guitar, so to make sure it looked good. He did a fine job, in my opinion.
As far as hearing a difference, I agree with you. Clean sounds better but distorted is great too. It blew me away that a note at the top of the neck could be so out of intonation when played at the bottom. He showed me before he did my guitar and I tested it after. Night and Day. Literally. The thing sounds incredible. HIGHLY recommended.