Yes, Alembic basses built as fretless will have the postion markers where the frets would have been. (At least every one that I've seen.) (Unless you request something different - they are the ultimate in custom, right?)
A way to think about it: The position markers are to help you see where to put your finger. On a fretTED bass, you put your finger between the frets. On a fretLESS bass, your finger essentially becomes the fret, therefore the position marker needs to be aligned where the fret would have been had it been there but wasn't because it's not.
(Sorry, got carried away there for a minute....)
C-Ya...........wayne