from what i've seen, it doesnt effect gameplay per se, what it does do is things like increase the time your offensive line will have a false start animation and therefore increase the amount of times that penalty- so when you talk about it effecting gameplay, what exactly do you mean? so far for me i have been quite impressed with how much the animations match up with the penalty flags, like when a defensive back will stand in the way of my receiver and impede his progress forward, preventing him from making the catch, i get really pissed off and yell "thats interference!" lol, but then they (usually) throw the flag, which i think is pretty sweet.
if you watch an NFL game, there are usually anywhere from like 9-15 penalties called, they are a huge part of the game and have huge impact on its outcome, so i employ the same rule for my sim franchise. sometimes ill get like 5-6 called, other games there will be like 13-14, it can suck when they get called on you, but all in all makes the game a lot more enjoyable and much more like real life imo