I think legitimately the best idea I have is just to add years where players were meant to be backups as some kind of negative score (either -0.5 per season as a backup's rate, or calculate a number that is less of an approximation than that), and then add that negative score to their careers. Like Jim McMahon had 5 seasons where he was simply a backup who played either zero or one games. If we say he played about 10 games a season normally (since he never did finish a full season in the league), that would lower his careers wins over average to 8.26, and then with an extra 50 games added to his career (now 151 or about 8.5 16 game seasons), his WAA goes down to 0.875, which would put him in between Eli Manning and Cam Newton currently. It's not perfect, but it was something I was thinking about.