Curt,
I own 20 bass guitars of various marques, and I've never hesitated, regardless of age or vintage, to improve them or repair them to make them more playable to me. To wit:
I had both my '73 Fender Jazz Bass' and '79 Musicman Stingray's necks refretted and refinished.
I replaced the original pickups in my '73 Jazz with Seymour Duncans, replaced the original tuners with Schaller replacements, and replaced the original bridge with a Badass II.
I had my '74 Gibson Ripper completely refinished (it is a factory second).
Like a lot of guys here, I'm a player, not a collector. I play all my basses, and I could care less if someone thinks that I've ruined it by modifying it in some way. I'm playing the instrument, not someone else. If I feel it needs something to make it more appealing to me, so be it. If I were a collector I'd be more concerned about keeping things stock, but since I play my instruments, it is not a primary concern. The way I see it, these instruments were made to be played, not placed in a museum somewhere. Others feel differently, and that's cool. For me, I'd rather play it than look at it.
On the Distillate, if the only sticking point is the fingerboard inlay, I'd call Mica or Susan and ask them how much it would run to replace the fingerboard and/or fill in the inlays and sand it over. You might find that they can do it for a relatively decent price. You could also just buy the bass and have that kind of surgery done later when it's more financially feasible. finally, you could have Alembic replace the inlays with something more akin to your tastes, e.g. an oval or some other shape with your initials in another material. I haven't seen the bass on Ebay yet (I'm at work and our firewall won't let me see it), so I'll reserve further comment until I do.
Alembics generally don't go up in value - there have been many discussions on this in the club - but once used, they tend to hold their value at a certain price point (e.g., $900-$1100 for Epics, etc.). If you got the fingerboard replaced, I don't think it would detract much from the value of the bass - it might even add to it depending on what you do with it as it would be, in the eyes of some, an upgrade.
Again, best of luck in your hunt for the perfect Curt Alembic.
Best regards,
Alan