Playing with IG; but seeing some overly accurate QBs with the combined higher accuracy already in the set. I do believe that the QB ability is cumulative between IG and QBA. At default, there are a combined 100 points of slider value (which gives too good of a QB). My current set (39 QBA and 50 IG = 89 points). I'm not saying that '89' is a magic value or anything, but I don't want too go too far above or below that. In other words, the more you raise IG, you should lower QBA roughly the same amount.
Offsides at a high setting will make defenders more aggressive in trying to anticipate the snap count...potentially giving them a boost.
Holding at a high setting will actually cause linemen to hold more often, improving blocking (particularly on pass plays).
It's ironic that you mention M12; that is the game where the discovery that penalty sliders impact gameplay was found. At a simple level, penalty sliders trigger certain animations and/or actions to occur. The easiest to see is facemask where high settings will cause more of the aggressive grabbing tackle animations to occur (you can actually see them). Sometimes they are called, sometimes not.
I agree....I think that balanced sliders on All Pro will lead to more balanced results. In that vein, and after playing more with the new tuner, I am reducing both offsides and false start to 55. Long story short, O-linemen were getting too good of a jump and were getting too much of a push at the line. Lowering offsides so d-linemen don't get too good of a jump.
Version 4 - Gamma uploaded to OP.