@zee-eff-ess I wrote an article earlier that summarizes how the rw filesystems work and are maintained across updates.
In short, /etc is writeable; /usr/etc is not - it is delivered with bootc image layers for whichever system you have booted. Details are in the article …
Remember /mnt is a symlink to /var/mnt (in case that matters). Although I have read others here suggest that mounting to /mnt does not work, I haven’t tried it.
The files in /etc, including /etc/fstab - as described in the article above - can be managed as usual. There are tools available (commands also mentioned in the article) to detect when /etc contents have varied from /usr/etc.
I use a NAS also - OMV in my case. I just connect to shares when needed using the Files GUI. I also have rsync end points configured for backups.
Back to your questions:
Just edit /etc/fstab as you normally would. I would keep a log of these kinds of changes to simplify the reinstall process though.
Try mounting to /var/mnt if you find /mnt to be problematic. But why not ~/mnt? Or /usr/local/mnt ?
The article linked to above references the official docs for ostree and rpm-ostree. Those are a treasure trove of info. I am pretty sure that is (at least part of) what you feel you are missing.
I know I did.