The premise, in short, says the 49ers have eliminated sight-adjustment routes from the playbook, instead building into the offense alternatives against blitzes by design, not simply in reaction to what the defense might be doing. This is spot on, and a reflection of what Harbaugh learned from Lindy Infante during his days as the Indianapolis Colts' quarterback.
I've tried to explain those Infante-based roots at various points. Brown's piece has brought into focus the application of those coaching principles. And, as joe_cool35 noted in the comments section, Eric Branch of the San Francisco Chronicle has covered some of this ground as well.
The changes Harbaugh has made are not specific to Smith. They are philosophical. The Green Bay Packers are using similar principles to an even greater degree. The 49ers would be using the same concepts if Aaron Rodgers or Peyton Manning were their quarterback. They are running their offense, not an Alex Smith offense, independent of whether or not the team would be more pass-oriented with another quarterback.
The approach suits Smith well because it eliminates doubt about whether or not the receiver has seen the same thing and reacted the same way. Smith knows what the receivers are going to do before the snap. He adjusts based upon what he sees from the defense. He should not have to wonder whether or not the receiver read the defense the same way he did.
"If you are in a three-step tempo to one side of the field, you could run a three-step tempo to that side, check it out, if it's not there, you are in rhythm to a five-step tempo to the other side," Harbaugh said when I asked him about the concepts during training camp. "Or you could go a five-step tempo to this side, check it out, it's not there, then come back to the other side of the field, you didn’t take any more steps, but you are still in seven-step timing on a five-step drop."
Smith's college coach, Urban Meyer, has long maintained that Smith is at his best when he's comfortable with every aspect of an offense. Some of the NFL's top quarterbacks have similar mindsets. Manning, Tom Brady and others, including Matt Hasselbeck, also covet more certainty. Others -- think Jay Cutler and Brett Favre -- have an easier time cutting loose.
The principles Harbaugh and his offensive staff have implemented were new to Harbaugh when he signed with Infante's Colts in 1994. Infante had expanded upon the option-route concepts Don Coryell used in San Diego.
I'm not certain how the 49ers are using these concepts, but the basic idea is relatively simple. Let's say a receiver has two options on a route. If the quarterback doesn't throw to him on the first option, the receiver goes to the second option. Either way, the quarterback knows the options and throws the ball when he's comfortable with what he sees.
"You could be reading two receivers," Harbaugh explained. "They are in a principle, say, a 'go' and then you come back to a deep option route. Five-step tempo back to a seven. If it is open, you throw it. If it is not open, I come back. It's open or it’s not."
One key for the 49ers and other teams using these concepts is to make sure the the routes designed to beat blitzes don't compromise the offense if the defense plays coverage instead.
For example, let's say the offense is facing facing third-and-7. The play might feature longer routes on the front side, with slant routes on the back side. The longer routes would be set to five- or seven-step timing, but if the quarterback noticed trouble quickly, he could still throw the slant on a three-step drop. But you're still running slant routes on third-and-7.
Smith has 10 touchdown passes and only two interceptions this season. He had eight touchdowns with one interception while posting a 3-2 record in his final five starts last season, before Harbaugh arrived. For that reason, I wouldn't attribute all Smith's success to Harbaugh or eliminating sight adjustments, etc. But if Smith appears more comfortable with the offense, the changes are very likely playing a role.