Comment # 1 on bug 1065040 from Andreas Stieger

I think Werner will know about this, maybe there is some configuration that can
be used in this case. 

Also /usr/bin/pinentry will select the pinentry to use based on installed
packages and the environment, is there something that can be used to detect
being called from within emacs?

security:privacy/pinentry builds pinentry-emacs, can you try that one?