This misfeature is going to go away soon, and it will always look in /etc/mt-daapd/mt-daapd.conf, then /etc/mt-daapd.conf and then fail.
Erm. Would it be too much to ask for mt-daapd to honor –sysconfdir=
when doing a configure? I mean, that’s the way most other software behaves and you could still check for configs in /etc/mt-daapd and /etc if you’re so inclined.