Found it’s simple to properly customize the email sending address of a system user account that an app has configured as a “resource” in its manifest:
yunohost app setting <APP> mail_user -v 'name'
yunohost app setting admidio mail_domain -v 'domain.example.org'
yunohost tools regen-conf postfix
# check:
cat /etc/postfix/app_senders_login_maps
yunohost tools regen-conf dovecot
# check:
cat /etc/dovecot/app-senders-passwd
If receiving emails is also desired, that address can simply be configured as an alias for an existing user (mailbox).
If a yunohost app package re-generates (overwrites) your entire local configuration file on upgrades, that package may at least have to be adjusted to use __MAIL_USER__ and __MAIL_DOMAIN__ in the template to configure email (instead of __APP__ and __DOMAIN__, but as I don’t have any such app installed I can’t confirm that for sure.