[Peaches]

If a quarterback takes a shotgun snap and gives the ball off around 4 yards deep what's the difference in the qb being under center and having to take the time to turn and then hand it off at 3 and a half?
Also, if you are in the gun all the time why risk a bad snap under center at the most important part of the field?

The most obvious reason is that you will automatically have an additional 4-5 yards to cross the goal line. In the shotgun the running back is also not moving towards the line of scrimmage when the ball is handed off. On the snap the defense is starting to clog things up and the more time you wait to get the ball moving in a forward direction the dirtier the path becomes. If you are under center you can either have the QB go up the middle immediately preventing things from dirtying up with a back pushing for help if needed. Another option is that the QB can hand it to a RB after he has gained more speed and power from sprinting towards the line to potentially break arm tackles. A QB is not going to take a 3 step drop to hand it off unless it is a draw play.
If a team goes in the shotgun formation all the time and does not have a standard goal line package that they have prepared specifically for these situations then shame on the Offensive Coordinator and Head Coach.