I have a gpg.conf-2 in my homedir. This causes the system wide configuration in the appimage under /etc/gnupg-vsd to be ignored.
To reproduce create an empty gpg.conf-2 file in your homedir and check that system wide config is applied:
aheinecke@hopper /t/appimage-gnupg.RWMENKlZuS> export GNUPGHOME=$(mktemp -d) aheinecke@hopper /t/appimage-gnupg.RWMENKlZuS> gpgconf --list-options gpg ... compliance:16:2::1:1::"gnupg::"de-vs ... aheinecke@hopper /t/appimage-gnupg.RWMENKlZuS> touch $GNUPGHOME/gpg.conf-2 aheinecke@hopper /t/appimage-gnupg.RWMENKlZuS> gpgconf --list-options gpg Monitor:1:0:Options controlling the diagnostic output:0:0:::: ... compliance:16:2::1:1::"gnupg:: ...