I just read through your build diary, and found the dot-on-fretless discussion really interesting. I am converting one of my basses (very slowly) to fretless. It's different than yours, because I pulled the frets on a rosewood board. I then filled the frets with a light colored hardwood veneer. I didn't fill the dots, but one of the advantages of filling the slots with veneer is that you can see where the frets were. Different than yours, but it got me thinking...
...why a dot? Why not a slot filled with a little veneer? You would not have to have the slot cross the fingerboard like a filled fret slot. you could just put a little slot right on the top edge of where the fret would be and fill it with a light hardwood veneer. To me that would be more intuitive looking than a dot, since the "line" would show you where to "fret".
Just a thought...and probably not a particularly good one...