I'm not sure why they didn't burn the last timeout before the 2 minute warning... Stop the clock, get another stop, and the Falcons would be forced to snap before the 2 minute warning for a 3 and out. Not sure of the logic behind that move.
While I think your math on the clock/ downs might be a little off, I was calling for the same thing.... they should have taken the time out before the 2 minute warning and made Atlanta take another snap. Wouldn't have saved them very much time, but the move cost them about 20 wasted seconds.
The more I think about it, the more pissed I am about the refs. That was just terrible. This isn't even a, "Oh, they screwed Denver so bad!" kind of mad.... they were regularly awful and everyone suffered for it.