Tom Brevoort : "My memory of this, David, is that it’s something that we came up with together, though it’s quite likely that I was the one who suggested it when the question came up. And that’s likely a reflection of when I started reading the books. You see, for the first decade-plus of his existence as a character, Franklin wasn’t ever referred to as a mutant at all. Rather, his powers were clearly a result of his parents having been altered by cosmic rays (plus the additional factor of the energy from Annihilus’ Cosmic Control Rod that was necessary to ensure a safe birthing process.)
Consequently, Franklin’s powers manifested almost immediately, whereas mutants (at least up to that point) typically began to display their powers in puberty. It wasn’t until the “Days of Future Past” storyline in UNCANNY X-MEN where an older Franklin was among the survivors in the dystopian future that people began to consider him a mutant. Thanks to its popularity, X-MEN tends to swallow up a lot of unrelated characters and concepts—Longshot and his cast, Captain Britain and his cast, etc. But especially with the rise of Krakoa and the change in the status of mutants worldwide, that presented some challenges to us on the Fantastic Four front. Specifically, we didn’t think it made sense for Franklin to relocate to Krakoa, nor for him to be exempt from the laws of regular humans in the way the assorted X-Men characters were. So when the opportunity presented itself to separate church and state came up, we took it. I didn’t really view it as anything other that reasserting the original status quo, but clearly some readers of a more recent vintage assigned it greater importance than that. But as I said at the start, that’s kind of the luck of the draw. Somebody’s got to wear the black hat, after all."