The San Francisco 49ers won their Week 3 preseason matchup with the Denver Broncos by a score of 29-24 after falling behind 17-0 in the first quarter, but we all know that final scores of exhibition games don’t matter.

— What mattered to the national media: Peyton Manning went 10-of-12 for 122 yards and 2 touchdown, no picks.

— What mattered to the Bay Area: Alex Smith went 5-of-7 for 65 yards, 44 of which came on a touchdown pass to Vernon Davis.

— What mattered to the 49ers’ coaching staff: San Francisco escaped from the game pretty much unscathed, save an ankle injury for Ted Ginn Jr, who left the game after being dragged down from behind. He immediately hopped off the field on his good foot, and was taken to the locker room. Good news: the ankle isn’t broken:

Anthony Dixon also went down at one point, writhing and clutching his right elbow, but he was able to return and play the rest of the game.

Backup to the backup

— Jim Harbaugh named Colin Kaepernick as the primary backup quarterback earlier this week, and QB-2 came into this game with 20 seconds left in the second quarter and played his way into the beginning of the fourth. As usual, the offense changed dramatically once Kaepernick stepped in; offensive coordinator Greg Roman ran several option plays and Kaepernick wasn’t shy about letting it rip when presented an opportunity to throw. He finished with his best performance to date this preseason: 4-of-4 for 80 yards. One might wonder – with the speed that Harbaugh and Trent Baalke have added in AJ Jenkins and LaMichael James – how different this offense could look once/if Kaepernick takes the reins.

— Scott Tolzien came into the game with just under 14 minutes left in the fourth quarter and the competition for third-string quarterback began. Tolzien looked poised and accurate in his few passing opportunities, but the 49ers stayed with a run-oriented offense. He threw accurate passes to both tight end Garrett Celek and A.J. Jenkins, however both passes were dropped. Tolzien did throw a dart to Brett Swain on a slant, which would represent his only completion on a 1-of-4, 16-yard day.

— Josh Johnson stepped in with 7 minutes left in the fourth quarter. If this was Johnson’s audition to become the No. 3 quarterback, he might not feel so good about his future with the 49ers. A 10-yard scamper on 3rd-and-long was Johnson’s lone highlight, as he went 0-for-1 passing after overthrowing Celek, who was wide open for a would-be touchdown. What also might be telling – Tolzien came back in for the 49ers final drive, although they handed off three times and punted.

Cox corners the No. 4 spot?

Tramaine Brock and Perrish Cox have been battling throughout training camp for that spot behind Chris Culliver on the cornerback depth chart. After Sunday, it looks like Cox may have an insurmountable lead.

Brock saw playing time for the majority of the first three quarters and the Broncos did everything in their power to expose his weaknesses. Five passes were completed to receivers under Brock’s watch, including an Eric Decker touchdown. He let Matt Willis get past him for a long completion and whiffed on a tackle late in the third quarter that allowed Jacob Tammie to get all the way to the 5-yard line. Later in the drive, Brock got beaten by Decker in the end zone (Decker dropped the pass).

Cox was challenged fewer times by his former team, but found a way to make noise when the ball came his way. In the second quarter, he jumped the route and picked off a Caleb Hanie pass intended for Decker, returning it into Broncos’ territory. He looked much better than Brock in coverage; at times he looked even better that Carlos Rogers. Stock rose on Perrish Cox considerably.

Alex Boone at right guard, Leonard Davis at tight end?

Alex Boone took all the snaps with the first-teamers at right guard, and he appears to have the job locked up. Frank Gore and Dixon got very little done behind the starting offensive line, rushing for 0 yards on five carries through the first quarter. However, pass protection looked much better, and Boone did his part. He gave up no pressures, and the times that Alex Smith did get flushed out of the pocket were arguably caused by Smith holding the ball too long.

Interestingly enough, it was tackle Derek Hall – not Leonard Davis – that replaced Boone at right guard in the third quarter. I spent a good 10 minutes scrambling to figure out what Davis’s number was (it’s not listed on the team website), wondering why he wasn’t in at that position. Davis came in later, switching off with Hall at the position. Both players looked solid, with Davis’s highlight at right guard coming when he blew out a defensive tackle on a big gain for Rock Cartwright.

The reason for Davis’s second-string absence? He was playing tight end on running downs, according to Matt Barrows of the Sacramento Bee. Could there be another tight end named Davis in the 49ers’ future? Coach Harbaugh liked what he saw:

“I thought there was a lot of improvement from Leonard today … really coming off the ball,” Harbaugh said. “He had some physical plays. I thought he got rhythm. He was just in sync today. Just better.”