Okay...just so happened I questioned CBN about this after his second year with us. I was at the Suit-em-up get together just before the season started at the French Press. He got around to dropping by our table and I asked him why he didn't have any plays under center, especially considering we had a couple of big backs that could hit the hole much quicker on short yardage downs. He started going on and on about zone blocking and RPO plays that keep the OL from getting downfield etc. etc. when I put my hand up and stopped him. I asked him if he thought Sean Payton was a top offensive mind/play caller. He said, yes he is pretty good. I then said, well if I had to guess, Drew Brees is under center 20% of the time, so why aren't more colleges doing that. At that point in the conversation, my wife told Billy she liked his haircut, which is the same as mine, just he has a full head of hair. He pointed at my head and we had good laugh.
But, the end of the story goes like this. A couple of games into the season, Billy had LL under center on the goaline for a play or two with a score. The very next home game during the Cajun walk, I waved at Billy and he immediately got down like he was playing QB under center. It was definitely cool to see for me.
Short yardage plays are tough due to the number of players the D puts in the box. The hole may be open only a split second and handing off to the RB direct from under the center gets him to the hole quicker than from the gun. With a FB leading the way, you can apply max pressure at the point of attack quicker as well, or simply hand off the to FB...which from my playing days was quick as s h i t. You had to be really quick to get the ball out from under center to make a safe hand off because the FB was on you in split second.
Regarding getting the snap from under center safely, if they don't practice it live, you are taking a big risk that snap will be fumbled. So, I can see why so many teams don't do it if they don't use it often enough to do it safely.
We never ran the gun with Coach Zeno, in fact I'm not sure if any college teams ran the gun way back in the 70's. I often wondered what that would have been like. All of our pass plays except for a couple were timed based on a 7 step drop. We always set up between the guard and tackle, left or right side depending on which side we were throwing to. We did have a couple of 3 step drops for slants patterns, but that put you close to the LOS and easier for D lineman to swat it down. Being in the gun would benefit the QB there as he would get the ball already at his set-up depth. One thing I liked about taking the snap under center is you always had vision on the defensive backs as you dropped back. Coach Zeno's offense gave us some easy reads against zone defenses and we always audibled out when they went to man coverage. Of course, that didn't happen to often back in the stone age. LOL!