Having a year in Martz's system is a huge advantage, even at a backup level. And JTO is a classic backup: he'll perform well enough in preseason against 2nd-string defenses (which is what happened against GB), but against first-string NFL defenses, his mistakes will eventually outweigh his positives.
As for Alex Smith, we've all heard the stories about how he needs to completely know the offense in order to be functional. Alex has been in catch-up mode since April, coming back from injury and learning a new offense. Right now, JTO has set the bar, and Alex needs to reach it (and surpass) as quickly as possible.
Again, it took a veteran like Kitna the entire preseason to feel comfortable with Martz's offense, so I'm not surprised Alex is still struggling with it. But if JTO is still the starting QB at mid-season, I'm guessing that Alex's career in SF is over.