No answer to [Whonix-devel] I2P Custom Router Conf yet.
It is important to mention that the Debian -- Details of package i2p in buster / Debian -- Details of package i2p-router in buster is being used since Debian patches configuration paths.
They had /etc/i2p in mind but it looks like it wasn’t completes by looking at debian/i2p.links · master · Debian / i2p · GitLab.
This is a problem. If the very file is modified that we ship than that will result in an dpkg interactive conflict resolution dialog.
Better to modify /usr/share/i2p/router.config. That one is probably not modified by the application. That file we can take over using config-package-dev displace. I speculate it will be used as a template and copied to /var/lib/i2p/i2p-config/router.config only once. Probably disadvantage: users won’t receive your changes to /usr/share/i2p/router.config when anon-apps-config is updated. At least not automatically / easily. That’s not easy without a proper .d folder.