That doesn't negate anyone from being a "system QB." And neither one of them ran basic stuff. They both learned a system, were allowed to grow in that system, and eventually mastered that system and ran that 1 systems the entirety of their career. (Brady tried Arians system before realizing it wasn't for him and going back to what he knew). Every successful QB in the league can be deemed a system QB. QBs aren't going around learning new systems every 2 to 3 years, at least not the successful ones.
Being a "system QB" doesn't mean you don't learn the elements of being a QB and that you don't know and can't master the element of the game. There are some things that comes with experience and that's what you are speaking to but if he didn't master the system/playbook,; do you believe that Drew could tell Meachem how to exploit that coverage? Let's get more specific; in the system that Sean Payton built around and for Drew, he exceeded everything that he did in San Diego. Is this saying that Drew didn't put in the work? Nope. Is this saying that Drew didn't eventually master the art of being a QB? He did (we had some rough patches though). Drew was allowed to fail and succeed in the system and in turned mastered it and knew every element and detail of it. The same goes for Brady and Manning and countless others. They master the system that they are in and that is something that all top tier and HOF quarterbacks have done.