To me the worse non-call was why the refs never called a single penalty for holding on that punt-safety. Jim H had no problem with the play itself, saying "you're coached to do that", and it makes sense. But a penalty while still getting a safety, stops the clock sooner, enough time that the Niners might - and I emphasize "might" - have given them time for a run back and one kick to tie it up.
I noticed the monster hold, too. But then I thought, so what? It's holding in the endzone, still a saftey. Nothing would have changed.
It WOULD NOT have stopped the clock sooner. The play would have still been run to its finish. They don't stop the clock just because there was a hold in the endzone. The play isn't blown dead then. They let the play run, then the 49ers would have had a option to take the play or take the penalty with the same result either way.