Hi Kick, nice concept with a few challenges.
Biggest one is the standard rosewood fretboard.....not many guitar makers other than Rickenbacker bother with sealing them, and these days Riccy's probably use Bubinga instead. The open porous grain structure would need a lot of filler to then allow the painted surface to stand a chance of working and not show premature signs of wear.
On my J Bass I bought some Black block fret marker stickers which are basically very thin vinyl sections that were stuck over an already Tru Oiled maple board with then a few more diluted TO coats on top to keep them in place. This could be an idea for the glossy 3,5,7,9,12,15,etc markers. For the matte black look underneath, Tony VH2580's idea of a very dark full strength dye or stain done first and then same stuff added to ebony timber mate to fill the grain but this will require some sanding to get a really smooth surface. A Satin Poly over the lot might work to seal things and retain some of the matte look.
There are also a lot of things around at the moment with 'Piano Black' trimmings and suspect it may be 2 pack epoxy type stuff. Not the easiest or healthiest stuff to work with.
Dedman's idea of an Ebony fretboard special order is the easiest solution as you can add shine in the desired sections and remainder is naturally dulled anyway, or a bit of light 0000 steel wool scuff sanding could help things along.