It may be because last November Rex had mentioned that he was no longer primarily focused on gameplay anymore and that he had creative oversight over the entire Madden franchise while gameplay was now primarily being handled by Clint.
Add in the fact that Rex seemed to be leading the charge for significant CFM changes paired with the nature of his exit and perceived direction that Madden is heading, and I think it's perfectly reasonable for someone to think that this move could have an impact on franchise mode. Most likely not this year, but certainly moving forward.