Where does Void Linux' Apache put its virtualhosts files then? I'm not familiair with an Apache instance which does not have a specific place for separate virtualhosts files.
In the Gentoo overrides, it's the same as vhost_root, i.e.: where Apache can find a configuration file containing a virtualhost. The Apache plugin uses custom-build, temporary virtualhosts for the challenge files.
I think it would suffice to use the /etc/apache/extra/ for both directory options. The vhost_files is probably fine: all configuration files have the .conf extension, so the file used by certbot should probably use that too.