I tested an upgrade from xenial to bionic today and did not receive a conffile prompt regarding /etc/cron.daily/apt-compat and part of the output you've pasted leads me to believe the file did not exist on the system which you were upgrading. Have you run into this any more?
Additionally, I've sorted out the issue in ubuntu-release-upgrader for Eoan. If you want it SRU'ed let us know.
I tested an upgrade from xenial to bionic today and did not receive a conffile prompt regarding /etc/cron. daily/apt- compat and part of the output you've pasted leads me to believe the file did not exist on the system which you were upgrading. Have you run into this any more?
Additionally, I've sorted out the issue in ubuntu- release- upgrader for Eoan. If you want it SRU'ed let us know.