I'm sure John was there so likely a true story.
Re the 390/375-4v and 390/401-6v, I have Dec 1960 and May 1961 Hot Rod where they discuss each. Lots of pics of mechanical linkage, nothing about vacuum even as a prototype.
The 430/400-6v MEL carbs DID have vacuum secondary & it would have made sense to plop them on there for the prototype 390/401.
BUT - the MEL carb have a "full moon" round air cleaner base, not the "half moon" FE style needed for the closer bore spacing.
So it would have taken a lot of hacking to get the MEL 6v carbs to fit the FE.
I do have a pic of a 390/375 what looks like a prototype, with VACUUM advance distributor, and of course that went away in production.
The vac advance 6v made more sense for an automatic car but since Ford didn't offer that (until later with a much milder cam in the Bird) maybe they figured cheaper mechanical linkage was plenty good, or even preferable for a stick car.