Wjen avahi is compiled with mdnsresponder compat layer, netatalk uses it and not the native API, even if available.
It should use the native API by default, and fallback to mdnsresponder, to avoid this kind of logs (gentoo, avahi 0.6.31, netatalk 3.1.6) :
Dec 14 12:01:01 krasus netatalk[22576]: *** WARNING *** The program 'netatalk' uses the Apple Bonjour compatibility layer of Avahi.
Dec 14 12:01:01 krasus netatalk[22576]: *** WARNING *** Please fix your application to use the native API of Avahi!
Dec 14 12:01:01 krasus netatalk[22576]: *** WARNING *** For more information see <http://0pointer.de/avahi-compat?s=libdns_sd&e=netatalk>
Dec 14 12:01:01 krasus netatalk[22576]: Registered with Zeroconf
When avahi is compiled without the mdnsresponder compat, netatalk works fine and uses the native API.
Related gentoo bug : https://bugs.gentoo.org/show_bug.cgi?id=492716
A patch for this is available on the mailing list at https://sourceforge.net/p/netatalk/mailman/message/34528188/
Pushed, thanks! Change is [6de3368].