I''m not a huge fan of defretted basses. Partly because of the looks and partly because the dots end up in the fretted positions. But in the "go figure" department. I have converted several perfectly good SX basses to fretless but did it by changing the fingerboard so they came out unlined. It was pretty easy to do and I bought some real ebony fingerboards back when you could still get them for under $50 each, while my Carvin AC50 is lined and has dots in the fretted positions so looks like a cheap defret instrument. It cost me over a grand.
I've always preferred clean fingerboards to lined ones, although if the bass comes from the factory lined (like the old Eko BA-4s), I won't mess with it. So when I do a defret, in addition to removing the frets I also drill out the top dots. I use a combination of sanding dust and super glue to fill the fret slots and dot holes before I do a final dressing on the 'board. The result is not invisible, but comes darn close.
For side markers I use 1/4" adhesive dot labels.