Now having said all that, what is the upside of the custom frame? It is all emotional. There is the feeling of being pampered, cared for by the builder. There is the visual appeal which you perhaps would have had a hand in creating. There is the uniqueness, rarity, and name recognition. There is the mystique. And I am sure a lot of other similar things.
This is mostly true, but lets also not pretend that all those things that make the super high tech frame "better" amount to much more than an emotional decision as well. They guy replacing his 2005 frame with the latest and greatest from 2014, while getting a technically "better" bike is making an emotional decision too. Will he climb faster or get to the coffee shop faster than his friends? I seriously doubt it. Even in the TT world where shaving seconds really counts the frame is secondary to helmet, wheels, position and other factors.
So let the guy enjoy his custom bike. It might be technically lacking by some computerized analysis in a lab, but if its built by someone who knows what they are doing it will ride just fine. He gets to pick exactly how his bike will look, choose his components, and watch his bike come together into a one of a kind machine, exactly how he wants it. I don't recall any claims of this being the "best" bike you can ride - not everyone needs or cares about buying what is considered technically "best".