The deal happened a few months ago and agents from around the league have made it clear that they are hoping strenuously that Colin Kaepernick’s extension with the 49ers is not a trend-setter.

Kaepernick gave the 49ers an extremely reasonable deal when he could have pushed for more, which I believe now puts the responsibility squarely on the 49ers to make good on the larger goal.

More to the point: Kaepernick could have played by elite quarterback rules and demanded huge up-front money. Quarterbacks normally don’t worry about their team’s financial principles.

But Kaepernick came to the negotiating table willing to accept the 49ers’ parameters and playing by the rules they’ve set up for the entire roster.

If I was in that position there’s no way I would’ve played by my employer’s rules. Jim Harbaugh wouldn’t do it this way if he was in Kaepernick’s spot and Harbaugh won’t do it this way whenever he negotiates his next deal.

So Kaepernick chose the team-friendly/49ers-structure way when he didn’t have to. He did them a favor at a moment of fairly high personal leverage.

Now the 49ers owe him something in return.

Fact: Kaepernick’s deal is theoretically worth $126M with some very nice top-end salaries down the road, but he’s only guaranteed $13M (with a $12.3M signing bonus), a very low amount for a young starting quaterback.

He gave up a lot of potential up-front cash, the kind of signing bonus and guaranteed cash that top-tier QBs ALWAYS get. As a result, the 49ers now have lot of cash freed up. The money they didn’t have to give to him as a big signing bonus is now burning a hole in Jed York’s pocket.

It’s not a cap-friendly deal because future big salaries still have to be accounted for in all cap calculations. But it’s an extremely cash-friendly deal for the 49ers. Usually teams pay out large bonuses to quarterbacks and spread it out over a long period to soften the hit, which means they’ve essentially guaranteed that they’ll keep the quarterback for that long period (or else the bonus will accelerate on their cap).

Instead, Kaepernick gave the 49ers the money to use right now.

And this all is happening just as the 49ers are staring at a gusher of cash from their Levi’s Stadium opening, by the way.

They have enormous new reserves of cash. Kaepernick cut them a break by settling for settled for $12.3M when he could’ve asked for $20-30M up front.

For me, the implication is now obvious: The nouveau riche 49ers have a responsibility to Kaepernick and the rest of the roster to pour some of this cash back into that roster, and right now that means Alex Boone, the underpaid right guard who is holding out.

There is some annual risk for Kaepernick, starting next April. The 49ers aren’t likely to cut him any time soon but this deal gives them the right to.

And what if Harbaugh leaves or Kaepernick suffers a minor injury that throws off his mechanics? What if things go sour in 2016 and the 49ers change regimes? Maybe there goes the rest of all that money.

It’s not likely, but it’s something elite quarterbacks usually do not have to worry about because of the huge bonuses they receive.

Cincinnati’s Andy Dalton was taken in the same draft in the same round as Kaepernick and just signed a similar pay-as-you-go deal with the Bengals, except he got more guaranteed money than the 49ers quarterback.

Compared to Kaepernick, in real guaranteed dollars, Dalton’s deal is much better.

But I’ve recently been told that Kaepernick absolutely was aware of all of this and that he was fine with putting his future salaries up for grabs, based on the 49ers’ decision every April 1 from now until 2020.

Kaepernick had to purchase a $20M disability policy payable to the 49ers, because the contract is guaranteed $61M for injury. Frank Gore did the same thing earlier and other players have done it for other teams, which I’m told is a product of a CBA quirk.

But Kaepernick has confidence in himself and felt he had to play by the same salary rules as his teammates because he didn’t want to separate himself from the group. He believed by doing this he was freeing up cash for the 49ers to give to other players.

That would seem to point directly to a player like Boone, who is fairly vital to the cause and probably would be amenable to a small bump in pay as long as it’s guaranteed into the future.

Under his current deal, with roster and work-out bonuses, Boone could get up to $1.79M next season.

Here’s an easy cash compromise: The 49ers could pay Boone an additional $1M in cash right now (he’s already guaranteed $2M if he is on the Week 1 roster), waive his fines for holding out, and extend him one year at a better, non-guaranteed salary to flatten out the cap hit.

Boone can come in with some dignity and an extra bit of guaranteed money. All it costs the 49ers is some cash. Which they have.

They could do something similar with Vernon Davis at some point, though obviously that would take more money than I’m suggesting for Boone.

The 49ers have so far not done either thing although they did recently re-do Joe Staley’s deal. signing him through 2020 and giving him $12M more than they were originally set to pay him from 2015-2017 (according to overthecap.com).

This is what the 49ers have to do to keep this roster together and they have to do it even more now that Kaepernick did them the favor of taking less up front and giving them more to pay out to his teammates.

If the 49ers pay it out.