I've probably ridden that combination, possibly not with the extension involved. I would probably try to get him to go for a threadless and in the larger diameter, but I suppose that is a conversation that has already been had. As far the the threadless is concerned, even such lugs icons as Richard Sachs use them.
http://www.flickr.com/photos/9866331...n/photostream/
They don't adjust as easily as the quill stem you are speaking of, but normally the stem gets left in one position after a while. If that is going to happen here, then it may as well be decided before the custom build is undertaken, and built out as needed.
Another option is to allow the head tube to project above the lug, and sleeve that extension, then you get a higher take off point for your quill, and it will be solid. You maintain the possibility of adjusting the stem and yet it is supported above the normal position. That would work so long as the adjustment isn't going to be the full 4 inches, which would seem to me to be a little odd.