If you think in terms of a factory built bass (Fender, Ibanez, Yamaha, MusicMan, etc.) the dots, inlays, fret slots, neck bolts, routings, all that stuff is pretty controlled. The side markers go on the neck based on a fixed design. Since fretless necks are a very low runner compared to fretted there's no cost incentive for a factory to make a different neck build just for a 2% item. For a hand-built instrument the builder has more flexibility. Best thing to do with side dots in "fretted" location is to use them like a landing light. You learn to adapt pretty quickly. Yes, it's kinda goofy to think of it as something that you and the factory know is a little nuts. Personally I just see it as a "humanizing" element. It's an imperfection that you can learn to love or ignore but short of paying premium it is something that's quite common.
Some brands get it, but most don't have any real reason to change.
Not in my experience. I've never played a factory fretless where the markers were between the frets (like on a fretted instrument). In EVERY case, and we're talking dozens of factory fretless basses here, the markers were where you place your finger - where the fret would go.
I've only ever experienced fret markers between frets on a fretless when it was a custom job after being built fretted originally, which is obviously a side effect of converting from fretted.