If (part of) the premise of the "Join or Die" policy is to regulate rogue "spellcasters" who otherwise would give all magi a bad name, then it makes complete sense to have a policy to deal with powerful non-Gifted persons. (Shades of Larta magi, which I still use).
But I don't see this as contradictory in the least.
If B based his theory on a "proto-Hermetic Roman Tradition" (for lack of a better turn of phrase), or (more likely) just did so in large part, the rest still works without change. He didn't adopt it wholecloth, he stole the name and adapted it to fit and expanded it with visionary genius - and that was a lifetime's work, and that was just to create the foundation that was then improved by others and over time.