Tim Kawakami is a columnist for the San Jose Mercury News. (San Jose Mercury News/TNS)

SANTA CLARA, Calif. — The San Francisco 49ers’ 2016 quarterback competition has been odd, it has been intriguing, and it might be coming to a swift and inevitable conclusion.

Simple facts here: Blaine Gabbert started the exhibition-opening 24-13 loss to Houston on Sunday and was decent, while Colin Kaepernick was held out with a sore throwing shoulder.

The guy who plays is almost always ahead of the guy who does not, especially when coach Chip Kelly has said the exhibition season will be the largest determining factor.

OK, it is not like Kelly is choosing between Steve Young and Joe Montana in their primes … or even between a young, unburdened Kaepernick and a playoff-proven Alex Smith.

But Kelly has to pick somebody to play behind center for the 49ers on Sept. 12 against Los Angeles, and every available sign points to Gabbert.

As it has from the start of preseason camp — or, really, from the spring, when it was clear that both 49ers management and Kaepernick preferred for him to play in Denver, except no deal could be hammered out.

It is kismet, then, that the Gabbert-Kaepernick duel could end in two practices and then a game Saturday against Denver.

If Kaepernick cannot participate this week, it is almost impossible to imagine he could make up that time; if Kaepernick can participate but is flat, it is just as hard to see him leaping over Gabbert as long as Gabbert is healthy and avoiding offensive cataclysm.

“Colin isn’t 100 percent,” Kelly said after the game, asked why Kaepernick did not suit up. “It wouldn’t have been fair to put him in and then judge him on that in the competition.

“We’re just trying to get him healthy and see if we can get him ready for this week against Denver.”

Kelly said he has been told Kaepernick probably will be ready for the Denver practices — which start today — but it is not clear if the 49ers expected Kaepernick to miss two practices last week or the game Sunday.

It is all blurry with Kaepernick and 49ers management (Kelly at this point is probably just a bemused bystander), and it has been like this for months.

And it is NOT blurry with Gabbert, who looked bad early Sunday but rallied to finish his three-series effort with a 43-yard touchdown pass to tight end Vance McDonald.

Gabbert was not special (4 of 10 for 63 yards and the TD), but he was running Kelly’s offense while Kaepernick was in sweatpants and a T-shirt roaming the sidelines.

“It was up and down, both Blaine and our first-team offense,” Kelly said. “I think that first drive, a couple balls he probably wants back, trying to get us on track.

“But I think once they settled down, got into a rhythm, I thought they did a really nice job of executing.”

So does Gabbert have a leg up in this competition due to Kaepernick’s shoulder soreness?

“I don’t look at it as a leg up,” Kelly said. “We’re just going to judge them on the opportunities to get in there and go.

“So if Colin gets in there and does a great job when he’s in, I’m not going to say, ‘Well, he didn’t get as many snaps as Blaine.’

“They’re going to be judged on who moves our offensive football team the best, who protects the football the best, gives us an opportunity to win games.”

Really, if a preseason game can show anything, this one was evidence that the 49ers’ quarterback issue is an offensive issue — they just don’t look like they are going to have much of a passing offense.

They will play up-tempo, they will spread the field, they will do what Chip Kelly always wants to do.

But if the 49ers are going to pick up first downs and score TDs, they will do it with Carlos Hyde and others running the ball and only occasional big-pass plays.

And they will almost certainly do it — at least to start the season — with Gabbert at quarterback, because he is more reliable, he is the darling of team management, and because Kaepernick is not healthy and definitely not the favorite of team management.

Beyond that, you have to wonder if the 49ers are thinking about putting Kaepernick on ice for the entire season, the way Washington sidelined Robert Griffin III last season once he lost the starting job to Kirk Cousins.

But that is a thought for a later date, when Gabbert officially is installed as the 49ers’ starting quarterback.

Which might happen in a few days, or a week at the longest, because it has been mostly inevitable from the start.

— Tim Kawakami is a columnist for the San Jose (California) Mercury News