I've found the Nikon AI an AIS manual focus zooms the be notably superior to most similar aftermarket copies, in accordance with your observations.
Yes of course, while computer aided lens design has been around since the 1950's, access to good computers and sophisticated optical design software was challenging for all institutions except the largest and best funded (and I'm sure Nikon was one of those fortunate large ones). Even today, options for optical design software capable of designing sophisticated multi-element lenses with relative ease, at reasonable cost, are limited. Zemax, for instance, was once a viable choice for smaller users, but through corporate acquisitions it has now moved to a subscription-based and very expensive pricing "model" - sort of a shame really. I remember purchasing the DOS Zemax version (for my employer) back in the early 90's for something like $900 and it was quite powerful even then.