Comment 6 for bug 156185

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.