I have a little bit of experience with this - I officiate high school football. Two points come to mind:
First, an official's whistle should never make the ball dead. You should blow your whistle after an incomplete pass, a runner is down, a runner steps out of bounds, forward progress is stopped, etc. A whistle in those cases is signaling that the ball is dead, but the act of blowing the whistle didn't make the ball become dead. Second, the worst thing you can do as an official is an inadvertent whistle. That is, blow your whistle when the ball is still live. In this case, the ball becomes dead, and one team is usually going to be pissed. For example, if team A throws a pass, an official blows the whistle while the ball is in mid-air, and team B intercepts the ball and returns it for a TD, team A will get the ball back and get to replay the down due to the inadvertent whistle.
Thus, when I officiate a team with an offense based on deception like the triple option, I will have a slower whistle. For example, if the B-back runs up the middle and gets tackled, I'm going to check and make sure he really had the ball (and not that the QB or A-back really don't have the ball and are streaking upfield). An inadvertent whistle in that scenario is perhaps the worst thing I could do. This isn't any sort of bias, but just making sure I get the call right. Again, the ball is dead by rule and not by my whistle. So in theory it shouldn't matter how long it takes me to blow my whistle after the play is over.