Hi Igor, first of all I beg your pardon that this was dormant for so long - 
just too many issues to pick from and NTP was long neglected for having so many 
issues we didn't want Delta but Debian didn't update. After Stretch was 
released NTP moved again in Debian, so if we need/want to change there as well 
it seems better now.
Also part of this reluctance is due to systemd timedatectl >> ntpdate 
(deprecated and causing all kind of trouble) and such.
Anyway - time to tackle things - and thanks for your debugging and suggestion 
already!

The particular change you suggested moves it from SysV to systemd which
is fine for Ubuntu, but might be an issue to Debian who still allow to
switch to SysV.

To re-triage the current state I checked this out once more on Xenial (as 
reported) and Artful.
Both still run systemctl from the generated service based on sysV 
/etc/init.d/ntp.

Just installing NTP has a running service after install:
- On both releases a invoke-rc.d ntp stop stops it properly
- On both releases a invoke-rc.d ntp start starts it properly again
- Rebooting (without ntpdate installed yet) works just fine, service running

Installing ntpdate and retrying:
- after boot the service is up in xenial and artful
- On both releases a invoke-rc.d ntp stop stops it properly
- On both releases a invoke-rc.d ntp start starts it properly again

Weird, unable to confirm or reproduce your issue.
But I remember we discussed and changed things around there - (waking up my 
memory).
Checking the ifup hook confirmed that - the stop/start is gone anyway in the 
newer release.

... Yeah memory was right I fixed that in Artful on the merge because
this thing was way more complex and error prone than its benefit - one
can check details at [1].

I need to backport that to X/Y/Z - preparing for that now ...

[1]: https://git.launchpad.net/~usd-import-
team/ubuntu/+source/ntp/commit/?id=943814aa43eb5915f4b643cd48061b3a7e4c75f8

** Changed in: ntp (Ubuntu)
       Status: Confirmed => Fix Released

** Also affects: ntp (Ubuntu Yakkety)
   Importance: Undecided
       Status: New

** Also affects: ntp (Ubuntu Zesty)
   Importance: Undecided
       Status: New

** Also affects: ntp (Ubuntu Xenial)
   Importance: Undecided
       Status: New

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You received this bug notification because you are a member of Ubuntu
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https://bugs.launchpad.net/bugs/1593907

Title:
  ntpdate startup routine prevents ntp service from launching up on
  Ubuntu 16.04 server on system boot; manually starting ntp service
  works: [FIX in DESCRIPTION], just need to apply it and release a new
  version

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