The reason why coaches don't just sneak it everytime is for two reasons I believe.

1 - the snap is different. In modern college football the QB is rarely directly under center. It's such a different timing for the center and QB that it significantly increases the odds of a botched snap if you don't practice it a ton, especially in that kind of moment. Staying in shotgun makes one less thing for the QB/C to think about.

2 - it's not as fool proof as one would think. Ultimately a QB sneak relies on those three interior lineman. Most teams in that situation are gonna have their DTs shade inside, have a N over center and then sink their LBs into those A gaps. This turns into 3 v 5 matchup. Being in shotgun is gonna keep the LBs honest and off of the line. Couple that up with us consistently getting a good push on their OLine all night and I can see why you might try and a run a longer developing play to see if you can create a hole through a different gap or with a guy pulling.

People have to remember that the reason the Philadelphia Eagles are so successful with the QB sneaks are because they have an all pro line and a QB that is insanely strong in the lower body.
But all of that is to say that there is still a really good argument to run a QB sneak in that situation despite my points. I'm only saying that it's not as crazy and illogical as some might think to not run the sneak.