Week Bogaerts switch positions with Story if asked? If not, and they extend him, aren't the Red Sox then wandering into the same pitfall their rivals in pinstripes did for years by catering to Jeter's need to be the starting shortstop while the better defensive (and offensive) player was right next to him? Story is obviously no A-Rod, but he's a better defensive SS than he is a 2B, or at least should be since it's his natural position. And how long do you extend him knowing that Mayer is only a few years away? If he's willing to move off SS, then I think it's a good plan. If he's not, it feels riskier.
What gets lost in most comparative analysis is how much better an offensive player Bogaerts is compared to other contemporary shortstops. The only really comparable offensive talent is Wander Franco and, sometimes, Tim Anderson. For all the hype, Correa, Seager, Story, Turner, Lindor and Bichette are really only slightly above average hitters in comparison.
The interesting dynamic here is that WaR, which nearly everyone uses for comparison nowadays, has a built-in inflation for the middle-of-the-defensive-spectrum guys, so objects in that lens are larger than they appear. So you need to look at some of the good old pure offensive metrics like OPS+ or wOBP for comparison of offensive skills. In fact, looking at collective OPS, the bottom four offensive positions are 1.) Catcher, 2.) Second Base, 3.) Shortstop, 4.) Centerfield, same as they always were.
So unlike nearly every other SS in MLB, Bogaerts has offensive skills that transcend his defensive position. He could move to a corner infield spot or to DH in a season or two without penalty to the offense. It's the same with Devers, who could easily move to 1B or DH to accommodate either Story, or in a year or two, Meyer and/or Yorke.