1) If you don't want to keep generations you don't have to: then no need to save
/var/guix/profiles or ~/.config/guix.
I personally skip them and only keep the formatted output of `guix package
--list-installed` under version control.
Note that /etc/config.scm can be stored anywhere, it does not have to be in
/etc/.

2) I don't use libchip, so I don't know.  How does it fail?  Can you provide the
backtrace?
Beside borg, other solutions include restic and duplicity.

-- 
Pierre Neidhardt