In speaking about the value of faceted stones, I think your faceting friends are talking about their perceived value, NOT about current appraisal practice. The drivers of value are demand and rarity (low supply) and this depends above all on color and to some degree (different with different species) clarity and of course carat weight. Cut is in there in the valuation as to how well the facets meet and how good the proportions are and how good the polish is. But custom cutting has never been an important valuation vector. At one point several years ago the Guide (Richard Drucker) had some advice in an issue which basically added about $150-$200 to a stone's value based on custom cutting. Faceters are not as organized as jewelers and haven't organized to push custom faceting. I think Drucker and other valuation mavens would be receptive to an organization which pushed on the value of custom faceting. At present you are at the mercy of the appraiser and what he thinks. Very few people, customers or jewelers, have seen a custom faceted stone side by side with a commercial cut one and so they think that one faceted stone is about the same as another, while this is actually true only from three feet.
You can market your custom cut stones by giving the jeweler or customer a folder which shows the stones color, clarity, cut and carat weight and also a GemCad diagram of the cut and the cutting instructions. This shows how the cu differs from the standard and also gives the customer a way to have the stone recut or repaired in case of damage. If you romance the stone in this way, some folks will see it as valuable compared to the run-of-the-mill stuff. If you show your stones side by side with the typical commercial cuts, particularly under the jeweler's microscope, they will understand why you ask more for it. There are also novelty cuts...initials cut in the table, ribbon cuts for the various ribbons for breast cancer, etc., the spider cut with the spider down in the culet of the stone, etc.,etc.
All this aside, custom cut is not an important factor in valuation and actually, some stones do better with a slightly less than ideal cut because a thick girdle, a belly in the pavilion and a high crown will yield more weight, regardless of the fact that they could detract from the stones optical performance somewhat. In the case of pale stones, a slightly less brilliant cut allows the stone to look darker and be graded higher.
With very good cutting available for $2/ct and the absolute top of the line custom cuts (to your design) at $6/ct, a faceter could make more money by using his superior rough buying skills and sending the rough out for cutting. the only exception to this rule, to me, would be expensive high end large stones where you might not want to trust the weight retention to anyone else. If the stone is $500/ct and you can save 1/2 ct, you've just gotten paid $250 for cutting the stone.
Forgive the rant, but you finally hit on a topic on which I do have some knowledge. Scott, if you want to come to the NC Frolic, get on the USFG faceters list, where news of the Frolic and all things related to faceting will be posted.