I am going to start by saying something that Niner fans will hate. Colin Kaepernick requires simplicity. I won't call him one read, I won't say he isn't accurate. I won't say he lacks intelligence. If I did, I would be lying. But he does lack an ability to scan the defense during plays and always pick the best option.
So Jim doesn't make him do it.
It's that simple.
Remember how bad Arizona made us look throwing the ball? Because our receivers are a bit small, they were able to line up a tiny cb, Jerraud Powers, 5'10, 187 on anyone but Kearse and not have a physical or speed mismatch.
Powers has no such matchup advantage vs either of the Niner receivers. So, the Niners opened the game in Arizona by going at that matchup about every other play. Powers played off Boldin, so three step drop and quick hit outside to Boldin, easy 8 yards. If Powers gets up on the line, Boldin throws him around in the 5 yard area and makes space that way, and they even ran a fly sweep wit the slow Boldin so Powers would end up having to tackle one of the slowest receivers to ever run a fly sweep. But they knew one thing about Powers, he doesn't really tackle well. In fact, he looked to me like tackling was the furthest thing from his mind. Point is, every one of these plays was a pre snap read. No scanning the defense, no moving the safety with eyes, just take what they are giving. Also, even after they stopped targeting Powers nearly every play, they went right back after him in critical situations later in the game. And almost always, it was a pre snap read. 6 of the first 12 plays they ran targeted Boldin on Powers.
So Harbaugh made Powers the target, and when Arizona adjusted, he went to the next easy to read and simplest read in the book, he targeted the linebackers spying his quarterback. SF would do what they do , lining up two or even three in the backfield with the QB, put those guys into pre snap motion, and see who on the D adjusted with them. Then flare one of those RB's out to the sideline after the snap. Didn't matter who, as long as it was on the side of the LB who had to keep eyes on Kaepernick. Kaepernick only has to figure out who the defense was ignoring so they could watch him, then make an uncovered throw. All pre snap reads.
While Roman's offense is incredibly complicated pre snap, maybe too complicated sometimes when you see how against the clock the Niners end up, the whole point of that is to end up with a play that will be likely to take advantage of what the defense is giving away on that play.
Two more plays that sum up how the complicated pre snap movement of the Niners is designed to give Kaepernick a single easy read. And take advantage of the spy assignment.
1st and 10, at the SF 36. Pre snap motion shows Arizona with man cover on the two receivers, with zone from the two middle backers (translation, Dansby and Washington are supposed to guard the middle and eyeball Kaepernick lest he run). At the snap, the RB, Dixon makes a beeline for the sideline, while Crabtree runs a meaningless route that sets him up to block the only defender on his side, Peterson. The linebacker eyeballing Kaepernick stays right where he is supposed to. Dixon is wide open. The feint to Crabree by Kaepernick is a front, Crabtree never even looks back at his QB, his job was to block Peterson. Easy one read catch, gain of 19.
1st and 10, at the AZ 30. Already in field goal range, this is the 6th time SF has lined up in a tackle eligible play, this time with Staley on the left side. As the play unfolds, Kaepernick appears to make a read to the right to Boldin, then spins left and completes a pass of 14 to Staley. There is no way the read to Boldin was real, he has 10 yards left in a deep curl route that he would never run against off coverage anyway unless he was the fake, and only on a trick play would the left tackle be the 2nd read. Like I said, it was a pre snap read, this play is intended to take advantage of the aggressive pass rush and the linebacker on that side intended to spy Kaepernick.
While I do think Harbaugh's offensive system is very well designed for Kaepernick's strengths and covers up his weaknesses, I also think that the compressed field of the red zone exposes some of the things Kaepernick is not that good at, as well as a lack of team speed at WR and RB, thus the high number of field goals for the Niners, particularly vs fast team defenses.