Seems like we’re thinking alike because I already did that back in May of last year when I had a mkinitcpio.pacnew file to merge and ran into some problems. In the course of fixing a ‘kms’ hook issue, I was also advised to get rid of Plymouth to get a glimpse on the startup and shutdown process/messages (which I prefer anyway).
That’s why I noticed the ‘Stop job’ blocking the shutdown in the first place.
I think that’s the crux of the issue. Upon revisiting our discussion, I was thinking to myself, what am I really looking an answer for. Turns out it’s not how to delete flatpak but understanding what caused this ‘stop job’/killing of xdg-document-portal.service.