Thanks for the great question. I ran a few games with a mix of edited QBs and non-edited QBs. Like you, I just believe that we can better overcome some of Madden's limitations by editing players. In fact, I'm of the belief that most ratings are simply too high and because of the pressure from real players EA inflates them. But that is something saved for another day.
While I believe that certain traits have an impact on home players actually play within the game, I don't think that there is much of an impact on QB accuracy. By changing the QB traits as I did, my hope was to cut down on issues where the QB holds the ball too long and "waits" to take a sack. By changing FORCES PASSES to IDEAL my hope was that the CPU controlled QB would be willing to make throws into tighter coverage down the field and not always check down.
The key take away here, I believe, is that on ROOKIE players play more to their actual ratings then at other levels. With everyone's input we'll be better able to learn what ratings matter and what impact, if any, various traits have.