Logic? There was no logic, but merely the ergonomic/perceptual benefit (to me) that comes from having a contrast between illuminated light green digits on a black background. I don't really like the segmented digits, either.
Atomic time synchronisation? I have no need of atomic time synchronisation - too much risk of passive X-ray radiation for my liking. If I wanted radiation, rather than get it from a radioactive Start Menu clock, I'd go visit a Chernobyl cafe and have a couple of caffè lattes whilst having a convivial chat with some of the mutated natives - probably a bit like visiting the Wastelands in Fallout 3. Of course, if I did that, then I'd not only be wearing a radiation-proof suit, but also I'd be watching that Geiger counter like a hawk.