IMO, it's all just what you are used to.
Since I started using a fretless seriously in about 1976, the only side marking normally available were either as shown in Kesslari's photo or the simple dots where the lines would be for the unlined boards. Initially, the only fretless instruments other than the factory Fender P (no lines), were instruments that we had defretted. Of course, those appeared as in the photo above. That was the norm, kiddies. Then in the '80's, there were the Pedullas, which were really the first designed modern fretless, a few Tobiases, and maybe a few others, but that was it. ALL of the Pedullas, Tobiases etc in that time frame had this marking. So, for me and a lot of other players that became the reference.
The first dot on line marking that I recall was somewhere in the mid-90's when Fender introduced a factory fretless J. And, that may well be the standard for a lot of current players. I never was able to adjust to that scheme. Never needed to.
Anyhow, back to the previous comment, the marking on the Zon is not a design flaw. Far from it. Joe has been simply making what his players are used to. I have no doubt he and other makers are now making whatever kind of marking the customer wants. Calling it a design flaw is inaccurate.