They did not have a solid prevent defense and were consistently beat over the top at the end. The safeties were playing 10 yds off and bailing however they were getting beat. By not forcing them to dink and dunk they never burned enough clock.
The SF run game only worked once they had their passing game going. Once the opponent knew they were running they had it stopped. However if they pass and get incompletions, clock would stop. My philosophy would have been to run it however I see the counter argument.
I don’t blame the bad snap / fumble on the coaches. Could they have called a play with no motion - yes however cross formation motion was fairly common feature of their offense.
In summary, I would expect a little bit of time working on a prevent strategy. Granted, this would take away time from other more commonly used defenses but that is the cost to developing it.