HiI also stumbled on the same. Chroot is not just a "non-default configuration" - it's been mentioned in Debian wiki since 2010:
https://wiki.debian.org/Bind9?action=recall&rev=1
A warning such as "You seem to run your bind9 in chroot, please do this
and that" during upgrade wouldn't hurt at all :)
Anyway, thanks for reporting this bug which saved me hours of troubleshooting!
-- Regards, Szymon
