It depends on how you define isekai. If A Connecticut Yankee in King Arthur's Court doesn't count, then Dr. Stone probably wouldn't either.
I personally prefer to place things into genres based on the emotions and themes that the works evoke rather than the technicalities of things like the setting. For example, I wouldn't consider Star Wars to be Science Fiction. Yes, Star Wars takes place in space and features advanced technologies, but the context is that of a fantasy rather than thinking about the specifics of how these technologies would work or how humanity might progress to that stage. So, it's more Space Fantasy.
I think the primary function of an Isekai is to escape the real world and to put ourselves in a different world or context where we can imagine ourselves having greater agency, power, and success than we have in our normal lives. That is the emotional beat we want to hit. So whether or not we are
actually transported into another physical or virtual world as the name of the genre implies isn't so important. What we really need is a relatable protagonist who serves as the audience insert (mundane in their original context) who becomes overpowered in their new life.
Dr Stone hits some of these beats. Moving thousands of years into the future where all of Earth's technology is gone is basically the same thing as being thrust in a new world, narratively. And Senku is definitely overpowered in his new context. But the fact that he's extremely knowledge about science right off the get go in ways that most audience members will not be makes him less optimal as an audience insert. And the escapism angle isn't even really the main appeal of the show. What makes the show unique is the science. The show is almost more educational than anything. It teaches us about the very important early technological advances of mankind and about how difficult science is as a process. We learn to appreciate all the work of humanity that took us to the present moment.
So that's kind of why I made the "Is a hot dog a sandwich" comparison. It definitely hits some of the beats of an Isekai, but it would also be disingenuous to call it "just" an Isekai. It's... Isekai-Adjacent?