(It got way too long for the ask box. This is both a HC and a fic idea.)
NWHS and the Bill vs. Dipper are two separate portal-related events. A few of the stories I’ve read that reference Author!Stan, it seems he had “passed on” by the time Mabel and Henry are married/have the Nibblets. I do see him, like Grunkle Stan, to develop a close relationship during the rest of the summer before Dipper’s assent into demonhood. I think because of what happened at the Transcendence, and the revelation Dipper isn’t dead (just a demon; I see that awful paranoia come ramming itself in his insecurities and trusting demon!Dipper versus human!Dipper, his GODAMNIT FAMILY I ALREADY WENT THROUGH THIS WITH MY OWN TWIN I’M A FUCKING ASSHOLE), he starts frantically researching ways to hopefully turn him back (failure is the only option), or at least make life much easier for Dipper (I can definitely see him being around for one of the Pines Parents meltdowns, going straight back into guilt because of his “RESEARCH”). I can see him helping Dipper and Mabel finalizing the different summoning circles (general public, research/educational institutions, family-and-friends-only, Gravity Falls version, emergency variants with less reliability) before all that stress, worry, and guilt from EVERYTHING finally kills him.
Still, despite that Downer Ending for Author!Stan, I think it would be more positive/bittersweet, since he expected to die alone after the 1986(?) Event, and he surrounded by family before moving on.
Maybe even one last conversation with Dipper in the Mindscape, and share a secret or two about his time as a Mystery Twin.