So what's your solution? How do we differentiate between a tablet user and someone who decided to shrink their windows?
As always, the issue isn't black and white. There is no solution that always works, because it depends on what you're targeting. If you want to scale elements to be easier clickable for people who might devices where it's harder to click/tap accurately, then "pointer: coarse" makes sense. If you're thinking about scaling elements on the website, some other solution fits better. Which one? Again depends on what you're aiming for.
I would want to check this empirically before accepting it as gospel. At least on the iPad, a mouse pointer is kinda halfway between a finger and a classic mouse pointer, and having to guess, my guess is that Safari doesn't change the designation just because there's a mouse plugged in.
And aside from that, shouldn't a tablet where a mouse is being used as the primary input show buttons sized appropriately for a mouse, rather than larger ones? The whole idea of making buttons bigger on mobile is to accommodate thumbs, so it seems like this media query is exactly what we should be using.