From an economic price/demand viewpoint, obviously they are not overpriced, or Alembic would close it's doors. However, I am willing to say that Alembics are indeed expensive from the perspective of the average musician. One must differentiate between cost and value though. When one considers the value of these instruments (playability, dependability, beauty, and resale value), the cost seems more justified.
One thing I have never been able to quite rationalize though is the price schedule for some of the upgrades. For instance, upgrading to an Ebony neck laminate is quite expensive. However, I know of other boutique builders where this is available at no cost. This makes me inclined to believe that the reason for the upcharge is probably not due to materials costs or labor (but I have never made a guitar, so what do I know? ). I have to think that there are other forces at work in Alembic's business model which would explain these factors. This is of course, just speculation.
Ultimately, I think what really makes Alembic unique is that they personally make almost everything on their instruments. How many other boutique builders make their own hardware and pickups? I am guessing very few.