There is a mechanism for asking questions before an install (debconf),
and ntp could certainly use debconf and mangle its own config files,
instead of marking them as dpkg conffiles.  As I recall, it used to do
so, actually, and the maintainers opted for a different approach at some
point in the last few years.

Ubuntu isn't terribly likely to deviate from Debian on this one (as
maintaining a retro-fit debconf patch on every sync can be tedious), but
you're welcome to file a bug on ntp in Ubuntu and in Debian asking for
debconf-managed config files.

To the usability argument, however, realistically, most people won't
ever have a changed ntp.conf (or even have ntpd installed), and
"usability" tends to speak of the "average user", not corner cases.
There are hundreds, if not thousands of dpkg conffiles in /etc, and
seasoned Debian/Ubuntu sysadmins (the sorts of people who tend to mangle
things in /etc by hand) tend to be used to dpkg conffile prompts.

-- 
ntp asks to keep or replace  ntp.conf
https://bugs.launchpad.net/bugs/156185
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