Hmmm... didn't you forgot to mention to change the user in the new pkg-message? Not sure if it is mandatory, and you point out to read-up about how to configure, but as you mention the FreeBSD team I would also mention to change the user. But as already told, I don't see a big showstopper, that's a detail which can be improved as time permits.

Looks ok to me. Anything which comes up as an improvement is IMO minor and can be fixed as a follow-up commit.

Please see my inline-comment for pkg-message.in, I think the text of the complete comment should be included. Please also remove the word "Desktop" from the UID file.

I also suggest to add a little text about the need for exec=on for /var/db/fahclient if /var/db is on ZFS and has exec=off.

FYI: in the past we had a folding@home client in the ports collection. It was named biology/linux-foldingathome. I'm not sure if this one should be done as a repo-copy from the old one or not...

Only reviewing the diff, I haven't tried on a real machine.

Please add something about linux_skip_mounts from https://reviews.freebsd.org/D22320

Under the assumption that the man page update will be added to https://reviews.freebsd.org/D22277: OK

Looks OK for me (after wrapping my head around PLIST_FILES and PORTDATA and how the port installs the files).