Turns out, both these files are special cases.
/etc/init.d/keyboard-setup was long obsolete - when Ubuntu used Upstart, there was an Upstart job for this, so the init.d script was never properly used. When Ubuntu moved to systemd, this should have been changed, but was overlooked. A post-release update added a systemd keyboard-setup.service, properly obsoleting /etc/init.d/keyboard-setup. If you install 16.04 from the original ISO and upgrade keyboard-setup, you'll see something like this in apt's output:
Obsolete conffile /etc/init.d/keyboard-setup has been modified by you, renaming to .dpkg-bak
(Not that you modified it, but ...) That's why there's a dpkg-bak file for /etc/init.d/keyboard-setup. You can ignore it. See LP#1579267 for details.
/etc/default/chromium-browser is weirder, because chromium-browser's postinst script actually deletes it out of hand:
$ dpkg-deb --ctrl-tarfile chromium-browser_70.0.3538.77-0ubuntu0.16.04.1_amd64.deb | tar x -O ./postinst
#!/bin/sh
set -e
if [ "$1" = "configure" ] || [ "$1" = "abort-upgrade" ] ; then
update-alternatives --install /usr/bin/x-www-browser \
x-www-browser /usr/bin/chromium-browser 40
update-alternatives --install /usr/bin/gnome-www-browser \
gnome-www-browser /usr/bin/chromium-browser 40
fi
rm -f /etc/default/chromium-browser
It has been this way since 2009. Some time in the dark ages /usr/bin/chromium-browser used to source /etc/default/chromium-browser, but now it sources /etc/chromium-browser/default (likely so that all chromium-browser config files can be kept in the same directory).
This missing file can also be ignored.