That's a sharp guitar, and I can see why you'd trust him to build something. You'll notice, though, that that's a 22 fret neck. Perhaps going to a 24 fret for you was outside his experience. It happens.
For instance, a buddy of mine had a custom guitar built up from scratch by a talented builder and had a similar issue...
You can't really tell from those pictures, but that's a 22 fret neck that was deliberately built to be a 21 fret neck. Buddy said "No! That's not what I asked for!" So, the guy somehow managed to tack on an extra fret at the very heel of the neck. You could probably knock it off just by yelling at it. Point is, when you're dealing with custom builders and asking for things out of the ordinary, you have to expect some anomalies. You don't have to take them, but a little forgiveness is sometimes in order.
However, in your case, the guitar might be unusable. In the above case, it was fine. Just less than ideal structurally.
Incidentally, that thing is made of about 8 different exotic woods and has some solid gold and jewels embedded/inlaid in it, and all that fanning on the back is Walnut in Curly inlay. I don't have any better pictures. Definitely a unique piece. There's Maple, Purpleheart, Ebony, Walnut and I don't remember what else in there. Weighs about 7,629 pounds. He named it "Gizmo", and the upper rear bout has an inlay of the little beast juggling a series of different colored Linde Star sapphires. Why? Nobody knows. Active EMGs. Some kind of bizarre pushbutton switching dingus. And, of course, the dreaded Floyd.