Even when Alex Smith wins, he can’t seem to win.

Coming off a 13-win season, more victories than he had in the previous four seasons combined, and a personal breakthrough as a pro quarterback, Smith has had something of a strange, tumultuous offseason.

First, he had to sit and wait as a free agent while his coach, Jim Harbaugh, took a strong look at Peyton Manning — despite Harbaugh’s strident (and ridiculous) denials that was what was going down — before earning a contract to remain with the 49ers.

Then Smith was caught in a strange argument in which he was trying to make a point about passing yards not equating to wins, one that ended up looking like he was calling out Cam Newton for being prolific but 6-10 as a rookie.

And now, after Smith served as Harbaugh’s caddy for the AT&T Pro Am at Pebble Beach in February, Harbaugh apparently will not return the favor when Smith plays in the American Century Championship golf event in Lake Tahoe, Nev. later this month.

The last part, of course, isn’t a big deal. But Smith did say Thursday, when I asked him on a conference call about whether the Manning courting lingered with him as motivation, that the situation was “a little awkward” when it left Smith in limbo for about a week.

“Certainly there are a lot of forms of motivation,” Smith said. “I guess that’s there a little bit as far as motivation.”

Smith eventually did sign a three-year deal with the 49ers, and he’s the unquestioned starter for now on a team that has clear Super Bowl designs and is armed with perhaps the best defense in the NFL. Better yet for Smith, the team went to great lengths to supply him with more toys at receiver, signing Randy Moss and Mario Manningham and drafting A.J. Jenkins in Round One.

So why does it feel as if it’s all on Smith these days?

Maybe people are not completely convinced last season was the start of an upward trend. Maybe people thought his statistics were good but not great. Perhaps it’s the notion that Harbaugh — excuse the phrase — caddied for Smith in the sense that he controlled his pitch count (Smith had the fewest pass attempts of any 16-game starter) and used creative formations and power football to account for the QB’s shortcomings.

Let the record show that public perception probably has little to do with on-field results. If Smith wins big again this year, he’ll likely get his due. And what matters the most is that Smith and Harbaugh maintain the same level of trust they had for each other a year ago. Harbaugh, in denying the 49ers’ work with Manning was anything but organizational I-dotting and T-crossing, was trying his best to protect his QB, and Smith said it never turned personal or ugly during the Manning courtship.

“I don’t think I ever had hard feelings for Coach Harbaugh,” Smith said. “It was a little awkward there for about a week, (when) I didn’t know what was going on.

“But I have a great deal of respect for Coach Harbaugh. He’s always been up front with me, always told me the truth, even if it was something I didn’t want to hear.”

Smith still hasn’t won over the 49ers’ faithful completely, even after last year’s flourish. The team is relevant again, and Smith had his breakout season at age 27. But he’s often viewed as passive and polite, perhaps not owning the edge to ever be great.

Harbaugh has vehemently dismissed that notion. Urban Meyer, Smith’s college coach at Utah who also was on the conference call, has been an unapologetic defender of the QB. And maybe Smith, having tasted pro success, is feeling more bold about his place in the league.

He sounded that way at times on the call.

“I certainly felt what I did last year, it was my job to compete for,” Smith said. “I really felt like I earned that right. I certainly wasn’t going to give it up to anybody, no matter who they were.”

Meyer defended Smith — and himself — by showing pride about watching his and Tim Tebow’s success last season play out in front of national audiences.

“To see Alex and Tim almost make (the) Super Bowl, I watched almost every frickin' snap,” Meyer said. “I love Alex Smith. It's great to see people you root for do well.”

Meyer now has three quarterbacks (Smith, Tebow and Newton, although Meyer might only root for two of them) who came from his programs the past several seasons who currently are starting or vying for starting QB jobs in the NFL. But Smith is perhaps closest to winning a title.

The 49ers, stocked with most of the roster of a team that lost in overtime of the NFC title game, are considered among the handful of teams capable of winning it all this season. Smith said it has required an attitude adjustment for a team that hadn’t finished above .500 prior to last season since 2002.

“Each and every guy in the locker room expects great things from us,” Smith said. “I think it’s a great thing. Yeah, it’s a bit different, but it’s great this way.”

Can he be the savior? Who knows? What Smith does know is that he doesn’t care about passing yards — hence the Newton thing, which Smith said he got “carried away with” — and QB ratings and all of the rest. Smith reemphasized that notion Thursday

“For me it’s about winning games,” Smith said. “I said the same thing last year when we played the Saints in the playoffs. Yeah, that offense is pretty prolific and (passed) for (more than) 5,000 yards. For me, I’m trying to score more points than the other team. I don’t really care how we do it.”

Smith said Harbaugh has made it clear that the coach thinks along those same lines.

“That’s our philosophy: We’ve got a lot of ways to get it done,” Smith said. “I don’t really care how many yards I throw for, as long as we score more points than the guys we’re playing.”

That’s the bottom line, it seems. But if the 49ers keep doing that, will Smith be beloved? That remains to be seen.