It seems like the prints of STAR TREK II: THE WRATH OF KHAN had the roman numeral added early on in its first run.
Correct. The earliest prints, for major cinemas, were 70mm (?) and a few weeks into the run, these were replaced by 35mm (?) prints (which did have the "II") - and the original ones went off overseas for our international premieres. A few weeks into the Australian run, we, too, had "II"s on our prints.