It’s important for any change to wpautop to have the minimal effects possible on other code and other places in the site, because there are a lot of interactions of this behavior with other plugins, often in surprising places, for example: Add Option To Turn Off wpautop - #5 by raygulick
One way this petition could work that would have the minimal effect in other places would be to add a new “group” of shortcodes that run at a different priority. For example, if wpautop runs today at filter priority 9, and then shortcodes run at filter priority 10, then we could add a new hook to run only the shortcodes with this new $do_wpautop = false parameter set, to run at priority 8 to avoid this issue. (Details to be ironed out and tested but hopefully that makes sense conceptually.)