SAN FRANCISCO — Apologies to Alex Smith. Really. Sincerely.

Last week in Green Bay, the 49ers quarterback was awful in the first half, threw a crucial interception in the second half and raised serious doubts (especially in this column space) about whether he could ever be an effective NFL starting quarterback.
Never mind.
Sunday afternoon at Candlestick Park, Smith reversed the equation. He reversed it so severely, some of us suffered whiplash. Smith had his best game as an NFL starter in a 20-3 victory over Jacksonville. He had zero interceptions, two touchdown passes and a sweet 96.8 passer rating.
What happened?
“I just feel better about seeing what I see out there,” Smith said afterward. “Understanding it, trusting it and pulling the trigger.”
Trigger-happy Alex? My goodness. There’s a phrase that none of us ever expected to use in a column about Smith.
However, as has been the case throughout this unusual season, the 49ers raise more far questions when they win than when they lose. And these were Sunday’s head-scratchers:
1. Has it really been the system holding back Smith all along, not his own play?
The performance against the Jaguars makes you wonder. After the Green Bay loss, Smith and two of his receivers — tight end Vernon Davis and wideout Michael Crabtree — had gone to the 49ers coaches and lobbied to open up the offense a little more, use the spread formation more often and not be as run-focused.
Much to the lobbyists’ surprise, the 49ers coaches didn’t kick them out of the lobby. Davis said that when the offensive game plan was presented to the team Wednesday morning, this was his reaction: “I smiled.”
The plan, you see, called for the 49ers to be more wide open, right out of the gate. Smith passed on five of the first six plays, three of them from the shotgun formation. The drive led to only a field goal. The tone was set, though. In the first half alone, Smith attempted 29 passes and completed 18, both career highs. Just as planned.
“But,” Smith said, “you still don’t always know what it’s going to look like come game day, how things are going to unravel. I thought we did a good job today, top to bottom . . .
“I still think we still left a lot out there.”
Hmmmm. The running argument among Smith-watchers has been whether his lack of progress as a pro has been due to his own shortcomings, or because the 49ers chose to limit his chances of flinging the ball. We might have received a clue Sunday.
2. Would the 49ers have a winning record if Crabtree had been with them the entire season?
Yes, it says here. Congratulations to Crabtree for showing up ready to play when he finally did sign his contract. But if the 49ers do miss the playoffs, some of the blame must still fall on his shoulders for holding out so stubbornly and stupidly.
Crabtree had four more catches Sunday. A couple of them were strong and sexy, worthy of his first-round selection. It’s impossible not to notice how much more space he’s created for Davis and the other 49ers receivers since he showed up in late October.
Crabtree also dropped a pass in the end zone on what Smith later called his best throw of the day. Because of that rookie muff, Crabtree merely had a good game instead of a great one. But if this had been his 11th game as a 49er instead of his sixth, he might not have dropped the pass.
3. How much of the 49ers’ defensive struggles have actually been the fault of the team’s short-possession offense?
The 49ers had superior possession time Sunday, which has been the case in all five of their victories. Only a fool would not make the connection between that and the 49ers’ defensive performances in those games, as well.
Numbers don’t tell you everything. But at least in the statistical sense, this team’s success is far more dependent on how its defense performs. In the 49ers’ five victories, the defense has allowed an average of seven points per game. In their six defeats, they have allowed 29.6 points per game.
One possible reason? When the 49ers’ offense goes three-and-out, by the second half, the 49ers’ defense goes onto the field with less energy. Dre’ Bly, making his first start for the team at cornerback Sunday, affirmed that theory while praising the 49ers’ offense.
“Any defense is helped by any offense that stays out there longer,” Bly said. “When the defense comes off and we sit there for 10 seconds, then have to get right back up ... that wasn’t the case today.”
4. If the 49ers fall short of making the playoffs, will they look back with regret on their early reluctance to be less run-fixated offensively?
They should. Of course, Shaun Hill was the starting quarterback in September under new offensive coordinator Jimmy Raye. But could the 49ers have done in September what they did Sunday?
“I don’t know “” that would probably be a better question for Shaun to answer,” Smith said. “But I think we’re fully capable of it. There’s a learning curve with it. The first year together, doing things, there’s always going to be some type of learning curve.”
The next and most important questions are whether the curve continues — and whether the Alex Smith who shows up next week in Seattle was the same one we saw Sunday at Candlestick. Fascinating answer to come.