I think it's partially because, like anything custom-made, it's a matter of finding the perfect buyer. It's easy to find someone who's willing to pay 2/3 of the price of a new one for a four-string sunburst MIA Fender Jazz; it's another entirely to find someone willing to pay 2/3 of the price of a new one for a 6-string, walnut top option, rounded body edges option, piezo-pickup option, mother-of-pearl block inlays option, etc, even if those two numbers are about the same. The more customized you go, the narrower the niche for the used market and the lower the resale value. Why buy used but not exactly what you want for 2/3 of the new price when you can get EXACTLY what you want, among dozens of options, for only a couple hundred more?
Also, because they are custom-built and have a 10-day return policy, I bet people who don't send them back right away tend to keep them for a very long time, rather than reselling. If you had a custom-made instrument that was perfect for you, why would you sell it, especially if you got a good deal on it? This, I'm sure, is compounded by the vicious circle fact that they have low resale value, so you're not giving up much by choosing to keep it rather than sell.
I suppose that's a good thing for Carvin, since it means they sell more new instruments. Still, it's too bad that people who don't have experience with them tend to think of them as somehow inferior. They are some of the nicest instruments I've played, electronics aside (which, as I said, are easy enough to swap).
IotaNet, I know exactly what you mean about buying a brand-new, custom instrument and then swapping the electronics. However, because they are factory-direct and so much cheaper, I personally wouldn't mind, since the money works out the same either way. They are really a semi-custom shop, not unlike Fender, etc.