We can see in your logs (thanks for all your effort BTW) that the failing cases 
are exactly those which have:
...
Server: 127.0.0.53
Address: 127.0.0.53#53
...

That represents the switch to systemd-resolved.

It might be worth to check (and if you want report) your output of:
  $ systemd-resolve --status

I guess we can already switch this bug from bind9 to systemd, or at
least add it.

Now one weakness of systemd-resolved that I've seen in several other bug 
reports is that - IIRC- if you have multiple DNS servers it does "the first 
wins".
So if you happen to have multiple DNS servers pushed via dhcp or other places 
what could happen is that one answers "SERVFAIL" before the other one could 
reply with a valid answer.

Is your setup using such a multi-dns scenario?

Info:
- There were some fixes in NM for that (bug 1624317) but I'm not sure if there 
aren't ways to still hit this.
- There are many, but one related upstream issue (for some context) is 
https://github.com/systemd/systemd/issues/6076

** Also affects: systemd (Ubuntu)
   Importance: Undecided
       Status: New

** Bug watch added: github.com/systemd/systemd/issues #6076
   https://github.com/systemd/systemd/issues/6076

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https://bugs.launchpad.net/bugs/1862437

Title:
  Ubuntu 16.10 & later, & derivatives do not query the assigned DNS
  server

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