Comment # 4 on bug 1088564 from Wolfgang Bauer

(In reply to Fabian Vogt from comment #3)
> If that's the only place, it's by design. No files in /etc/X11/ are ever read
> in a wayland session.

AFAICT, it is the only place.
And that explains why this has been reported as bug at all I suppose.

> The correct place is in /etc/xdg/autostart/, it also has the benefit of it
> being visible in the autostart KCM.

With gpg 2.1 or higher, gpg-agent should actually be autostarted on demand
though AFAIK.

See also bug#1050438.