delay of game

[DJ_NV]

Is there any benefit to the NCAA code as far as DOG? I'm not sure I like that the clock (if running) is only started on the snap if A is in a SK formation, but maybe someone can explain the logic that I'm not seeing.

Example: Had a play last weekend, about 1:45 left in the game and 3/10 for Team A who is leading by 3. They're waiting til the last possible second to snap the ball (there's a visual 25-sec clock on the field) and they're not in a SK formation. Clock gets to 00 and Team B is screaming for a DOG (something happened and Team A was confused about the snap right around :02 on the play clock but probably would've gotten the snap off at about a second or two after the PC expired. Again, Team B is screaming for a DOG so I give it to them. We march off 5 and then wind it. Team B coach goes nuts because we're winding it and I tell him that that's the rule because they weren't in an SK formation. So amazingly he starts yelling that it's a horrible rule (and not at me) because now they just get another :25.
Now the question is whether the R should've wound the clock on the RFP as he knew that A was trying to run out the clock but assuming they weren't intentionally trying to get a DOG? What if they were? Is it on the snap then?