SANTA CLARA, Calif. -- After the San Francisco 49ers' crushing Super Bowl LIV loss to the Kansas City Chiefs, general manager John Lynch and coach Kyle Shanahan made it clear that for as much as they'd love to keep the NFC champions together, it was going to be difficult.

On Monday, only hours after the Niners agreed to terms on a five-year deal to keep versatile defensive lineman Arik Armstead, they came to the disappointing conclusion that keeping one of their Oregon "twin towers" would come at the expense of the other.

San Francisco traded defensive tackle DeForest Buckner to the Indianapolis Colts for the No. 13 overall pick in the 2020 NFL draft. That deal won't become official until the new league year begins at 4 p.m. ET Wednesday but has been agreed upon, a source told ESPN's Adam Schefter. When it does, Buckner is expected to sign a new contract that will pay him $21 million per season, the second-largest annual salary ever given to a defensive tackle.

While the quick assumption would be the Niners chose Armstead, who has been less durable and productive, over Buckner, that's not really the case. In reality, the 49ers chose Armstead at a price of about $17 million per season plus the No. 13 overall pick over Buckner at a price of about $21 million per season. The flexibility that comes with a second first-round pick (the Niners also own No. 31) and some additional cap space means the 49ers will turn the Buckner deal into one or more talented, cost-controlled players who theoretically could extend their Super Bowl window.

Let us not understate what losing Buckner means: Without considering future moves and how they'll pan out, the 49ers are a worse football team than they were Sunday.

In four seasons with the 49ers, Buckner was a franchise pillar, the kind of player a team builds around and pays exorbitant sums of money to keep. Over the past two seasons, Buckner's 125 tackles and 18.5 sacks ranked second and third, respectively, in the NFL among defensive tackles, all while facing the sixth-most double teams. Buckner also has been durable, missing one game and playing 3,347 snaps, third most among defensive linemen since he entered the league.

None of that accounts for the fact Buckner was a team captain each of the past two seasons, earned the Len Eshmont Award given to the player who "best exemplifies inspirational and courageous play" in 2018 and the Bill Walsh Award, which is essentially the team's MVP, in 2019. Buckner was beloved in the 49ers' locker room, a point driven home by the outpouring of support from teammates on social media after the trade was announced.

To be sure, the 49ers have no obvious replacement for Buckner, who was a second-team All-Pro in 2019. There are players who could step in, including Solomon Thomas -- who is entering the final year of his rookie deal and has always been thought to be best suited to play Buckner's three-technique position.

But Buckner is a good enough player that the Niners can't simply plug someone in and have a defensive line as dominant as it was last season, when the foursome of Buckner, Armstead, Nick Bosa and Dee Ford held opposing quarterbacks to a QBR of 11.9 with 25 sacks, nine interceptions and three touchdown passes allowed.

That said, the Niners' decision to trade Buckner makes sense. The 49ers were going to have trouble signing all of their talented young players, with tight end George Kittle due an extension next and others, such as linebacker Fred Warner and offensive tackle Mike McGlinchey, coming due down the road. And while Buckner is undoubtedly a difference-maker, $21 million a season is a hefty price for any defensive tackle not named Aaron Donald.

Still, aside from Bosa, Buckner was probably the team's most valuable defender. Why not tag and trade Armstead instead? Or perhaps find a taker for Ford?

The answer comes down to value. Buckner's price tag clearly made the 49ers uncomfortable. When they had to take stock of how best to keep the bulk of their line together, it was obvious Buckner would fetch far more in trade than Armstead or Ford. He did, and the Niners now have two first-round picks, no small thing for a team that isn't scheduled to pick again until the fifth round after choice No. 31.

From the day Shanahan and Lynch arrived in the Bay Area, they've repeatedly pointed out that the goal is to achieve and sustain success. It's easier said than done, but the teams that do it often find themselves having to make choices like the ones the 49ers made Monday.

For the 49ers, losing Buckner means making yourself worse in the short term but creating an avenue to keep chasing championships for the long term.