They are commented out because they are mounted by zfs.
Is it stopping at this point or does it continue booting? If it continues booting, you can ignore that message. It is caused because the zfs mkinitcpio hook is trying to import the pool twice.
If you are getting past the initramfs I suspect your issue isn’t related to that error. It may not even be related to zfs.
I suppose booting has finished. It just stops at the manjaro default desktop background and does nothing else.
You’re probably right that it may not be related to ZFS, because I have full access to / and /home/<user>. I originally thought this was ZFS related because during the package installation process I saw this error
[2020-11-04T21:05:51+0100] [ALPM-SCRIPTLET] modprobe: FATAL: Module zfs not found in directory /lib/modules/5.8.16-2-MANJARO