Sean,
Just my two cents, as a casual observer with no particular interest in the outcome. I don't mean this to sound personally critical in any way, just some thoughts and even a couple of ideas that might help.
Personally, I think you're pushing your luck here. Alembic insists on relatively few things, like Alembic electronics, or not building you an instrument they know you won't be happy with, and to me it's perfectly reasonable they insist it go out with their logo.
Most of this is, in fact, because they care about their customers, including those who may own these instruments in the future. If it's important enough to you to own an Alembic, then I should think you would be willing to respect that.
I also think that in this case, size does matter. It's part of what makes it official, and there was some concern expressed about this in a discussion about Alembic jewelry (archived in Miscellaneous).
Now, I suppose if you're getting one inlaid - and one assumes it will therefore be there forever - maybe a different size would be barely acceptable, and maybe they already are smaller than the cast ones, I'm not positive. But hey, it's not like you just hit the zoom button and crank one out at another size - these are fairly intricate things, and a custom size is going to be a pain (and probably expensive).
So here are a few different approaches that come to mind.
First, you could just get the cast logo on the peghead and then remove it yourself. I don't know how they're attached (perhaps someone else will comment), but my guess is that at worst you might need to refinish the front of the peghead, and might get away with a small touch up or even ignoring it (the cast ones are clearly put on after finishing). I certainly don't advocate this, but it is your bass at that point.
Or, maybe Alembic would be willing to put it on the back of the peghead. Again, I'm just thinking out loud here - there are certainly some limits (e.g. let's not try for inside a coverplate), but it might be a simpler solution all around, including placing the logo in a sufficiently subservient posture.
I think maybe you're worrying too much about dust and dirt collection. If it's as bad as you make it sound, by the time you get the bridge cleaned, dusting off the logo won't seem like a big deal :-) In fact, if you just keep a small brush in your case, you could probably keep up with it pretty easily. Also, I find that with a silver logo positioned underneath silverish strings, it kind of blends in. Though it may be larger, it doesn't draw attention as much as an inlay. It's surprisingly subtle, and looks more like pewter than silver.
If you do go with an inlay, maybe you could tone it down a little without shrinking, by using a simple backing like ebony rather than the bright and colorful mother of pearl. I don't really know if that's feasible, but from here it seems like it might be simpler than some of the other ideas.
Just some thoughts to kick around, hoping you can get this worked out without much more difficulty. Good luck.
-Bob
Oh, by the way - the dove is generally quite nice, but my first thought on seeing it was that the poor thing had this branch going down its throat. Sorry, maybe I shouldn't have said that, but I think I'd prefer to see the branch going through the beak at an angle, coming out the other side, or something like that.
