If I can remember back far enough, the initial reason I went down the custom build route for my Strat was simply colour - I wanted a translucent black quilted maple finish which at the time wasn't available stock. As soon as I had, my discussions with the luthier lead to other subtle variations - the body contouring is slightly different, the neck join has been contoured slightly to allow better access, as well as a subtle larger scoop for the bottom horn. Also I wanted a fixed bridge.... I guess I am saying there are loads of ways to make a guitar just that little bit more personal that a luthier brings - and I think it's always great to have a 1 off :)
I would definitely do it again...just got to keep saving!