This looks like an unfortunate effect of the linux-rpi renaming and pacman's package conflict resolution process.
Check out the wiki page about pacsave files:
https://wiki.archlinux.org/title/Pacman ... nd_PacsaveThe process looks like this when installing the new 'linux-rpi' over one of the old 'linux-*' packages:
1. pacman sees that 'linux-rpi' conflicts with the old 'linux-*' so the 'linux-*' package is first removed (equivalent to "pacman -R").
2. "/boot/config.txt" is part of old 'linux-*' and pacman notices the user has modified it, so pacman backs it up and renames it to "/boot/config.txt.pacsave".
3. pacman installs 'linux-rpi' which happens to have its own '/boot/config.txt'.
Thus, installing 'linux-rpi' on a system with old 'linux-*' is not treated like an "upgrade" but more like installing an alternative, conflicting package.
As the wiki page says, the user is expected to handle the pacsave file, manually or otherwise. Yes, this does complicate upgrades on existing installations, especially automated upgrades, but this really is part of how pacman works. You'll just have to watch when pacsave files appear.