Error: Grub 'user error' not found

Probably. Then you at least has the encryption config right.
The other changes are cosmetic.
The hook changes are important, but they were introduced like an year ago.

Generally, users have to learn to take care of pacnew files in due time. Cause these come and bite your posterior after some time.
https://wiki.manjaro.org/index.php/System_Maintenance#Pacnew_and_Pacsave_files