The feeling among the staff could very well be that Herbert, at the very least, could deliver a few more big plays that increase the Ducks' chances of pulling off an upset. Plus, it's far likely that Herbert is far more comfortable now with the offense than he was a month ago, thus making it more likely he is ready from a mental standpoint.
But it would seem to make more sense, at least from this vantage point, to start Prukop, who has already played solid football against two ranked teams, then should he falter replace him with Herbert.