SANTA CLARA — Colin Kaepernick’s breakout game Sunday isn’t sparking a quarterback controversy on the 49ers. Instead, it’s created a mind-bending quandary for their opponents.

The WildKap offense includes a read-option package that helped spark the 49ers’ 34-0 rout of the New York Jets.

“That puts a lot of stress on your defense, to prepare for that week in and week out,” said coach Chan Gailey, whose Buffalo Bills (2-2) visit the 49ers (3-1) on Sunday.

It’s not as if the Bills defense needed more worries after Sunday’s debacle, where it allowed 45 second-half points in a 52-28 defeat to the visiting New England Patriots.

But the Bills must devote practice time to brace for Kaepernick. Alex Smith’s second-year understudy delivered a five-carry, 50-yard effort against the Jets, highlighted by a 7-yard touchdown run for a 7-0 lead.

“Now you give all the defenses around the NFL something they’re going to prepare on a lot during the week, which takes their focus off other things,” 49ers safety Donte Whitner said. “That’s a good thing for our offense.”

Whitner had a premonition Kaepernick would get unleashed Sunday, and he shared that vision last week while they sat together for breakfast at the team’s hotel in Youngstown, Ohio.

After preparing to face Tim Tebow and the Jets’ version of the Wildcat offense, Whitner asked Kaepernick how much the 49ers would significantly use their version of the quarterback-running scheme. Kaepernick replied that he didn’t know, but Whitner countered: “I bet you run it and you score a touchdown.”

Fueling Whitner’s confidence was watching Kaepernick mimic Tebow on the scout-team offense, not to mention Kaepernick’s sneak-preview displays in the exhibition season.

“He was actually playing Tebow when our defense was out there, and he was looking good,” Whitner said. “I just had a feeling he’d get out there and coaches wanted to show our wildcat on the national stage.”

Kaepernick’s spry legs offer an extra dimension that enticed the 49ers to trade up and select him in the second round of last year’s draft. Those talents were on display at the University of Nevada, where he became the only player in NCAA history to run for more than 4,000 yards and pass for more than 10,000 yards.

Said left tackle Joe Staley: “He’s always been fast. That was his thing coming out of college.”

With Kaepernick on board for 1½ years, it’s not as if the 49ers just created plays for him last week.

“This is something we’ve had in our offense since last season,” Staley added. “Kaepernick, with his skill set, he’s more explosive because he’s a little faster than Alex.”

Smith said it was great watching Kaepernick’s “extremely efficient” highlights when the 49ers gathered earlier this week for film review. Coach Jim Harbaugh used the term “extremely explosive.”

“He was just very efficient in his mechanics, and everything that he did out there wasn’t affected by being on a big stage,” Harbaugh added.

Shortly after Smith held his weekly media session in the locker room, Kaepernick emerged from the players’ lounge, grabbed his playbook from his locker and quietly strode past reporters without comment.

A day earlier, Kaepernick told the 49ers’ flagship radio station, KNBR 680-AM: “I’ve just been trying to work hard, and I’ve been waiting for my opportunity. It just happened to come that week.”

The WildKap will surface again. But when? That’s what the Bills and others must stress about in the future.

“He’s done a good job of running what they’ve put in,” Gailey said, “and they’ve done a good job of keeping it varied so it’s not the same.”

For more on the 49ers, see Cam Inman’s Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.