My first attempt to fix this involved trying to move gpg-agent invocation from 
upstart to systemd --user. I got that to work by creating:
~/.config/upstart/gpg-agent.override (manual)
~/.config/systemd/user/default.target.wants/gpg-agent.service -> 
/usr/lib/systemd/user/gpg-agent.service
~/.config/systemd/user/gpg-agent.service.d/override.conf ([Unit] 
Before=graphical-session-pre.target)

That correctly started the gpg-agent service, but the environment
variables were not visible within a terminal started from gnome-shell.
Somehow upstart seems to be the only way for setting env vars, the
systemd user service unit does not work as intended. Upstart needs to
die. Fast ;-)

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https://bugs.launchpad.net/bugs/1675925

Title:
  gpg-agent service sets wrong SSH_AUTH_SOCK value

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