As with any custom, I assume you will pay for choice of woods, neck shape, fret material/size, nut width, paint, etc. If you are OK with the Standard specs, there's probably no reason to pay extra for the Custom.
I've played the standard and the custom. Had an opportunity two buy either for around the same price and I went with the standard. I'm extremely happy with my purchase. I honestly couldn't tell a difference between playability or quality.