No problem Rob. I've never encountered problems with this before, which I guess is the point I was trying to make. For obvious reasons I tend to overthink things all the time so I can't exactly disagree with your looking into any potential problems of course! If such a problem was common, this is why I would use something like one of my PCB drilling bits to make a tiny hole which the spur of a drill bit would happily locate in. Running the lip and spur bit backwards to further locate itself centrally to the hole would maintain the accuracy.
To be fair (this is where I have learnt to let the clockspring of my thinking unwind) I think it will be a case of diminishing returns. How confident are you in the depth of nacre on your dots? If you have a spare one, file it down until it looks less-than-satisfactory so you know how far you can push them, I guess. They look a little thinner than the ones I have hanging around judging by the photo.
Meh, I'm starting to think too much.
Yeah.. I do tend to overthink everything a lot...
The dots are exactly 1.5 mm thick. On a 16" radiused board, the difference between the lowest and the highest part would be somewhat over 1.8 mm (outer edge), so I'm not sure.. I might just drop them in 0.5 to 1 mm below the surface.
. I used 1.2 mm nails through the nut area and the 24th fret. Then I covered up the truss rod (which is just sitting in without any glue, kit or tape, except the plastic tube around the rod that came with the TR) and put some Titebond on the neck. I removed the tape and put the fingerboard on, aligning it with the nails. I'm very pleased and happy using this method, because there's absolutely no moving around. Here's the neck and fingerboard with some clamps on it: