As for the ‘broken permissions’ issue - with the change recently made pamac moved away from using it’s own set of metadata - this should be gone.
Yes it has been annoying - but this doesn’t make pamac any less useful than other AUR helpers.
As for replacing system files - that is a no-go - but it is unavoidable - if/when - a package exist in AUR with identical name; even so the user may have replaced it intentionally.
If the stance you refer to is the unsupported nature then you are correct and this is in line with Arch Linux itself.
DISCLAIMER: AUR packages are user produced content. Any use of the provided files is at your own risk.
– https://aur.archlinux.org/
If you follow the link Learn more…
Warning: AUR packages are user-produced content. These
PKGBUILDs are completely unofficial and have not been thoroughly vetted. Any use of the provided files is at your own risk.
– Arch User Repository - ArchWiki
Generally speaking - as @cscs said
The AUR is not officially by supported by Arch - which it is aimed at - why would Manjaro support it any more than they do?
If one choose to use AUR - it should be a consentious decision based on needs - not based on a toggle with a minimal - easy overlooked warning.
Enabling AUR in pamac presents issues which may not be obvious to the casual user - hence the walk down memory lane in [Need-To-Know] About Manjaro and AUR
See below → RE: About Manjaro and AUR - #11 by linux-aarhus