I think they key point here is look. Many of us feel that the JEM is pretty much the perfect
guitar in terms of looks or feel or sound, but that we're unhappy with a few little aspects that can only be changed by having a copy of a guitar built with those few changes.
For example if I felt that the JEM played the best and looked the best, but I liked the sound of a mahogany body better, I have no way to obtain a mahogany JEM, Ibanez won't make one for me. BUT a luthier can craft me a body in the wood of my choice, maybe with better quality woods than those found on the guitars normally available. This would then mean I had the looks, the feel AND the tone I was after.
Similarly if I decided that I prefer a different hardware configuration, such as 2 humbuckers, a 3 way switch and direct mounted pickups, but still wanted the look and feel of the JEM because to me those are the ultimate look and feel for a guitar. Ibanez won't supply me with that guitar, but a luthier doing custom work can.
Again if I want a vine inlay on a guitar that has screwhead inlays, Ibanez won't change the inlays for me, but Jeremy at LGM guitars will
It's about going from being 99% happy with a guitar, to 100% happy. Some of us geeks here are willing to pay for that
I hope that answers your question