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

Status in bind9 package in Ubuntu:
  New
Status in systemd package in Ubuntu:
  New

Bug description:
  Starting Ubuntu 16.10 resolution of LAN addresses fails.   This name
  resolution failure is evident in every post 16.0 Ubuntu & derivative
  that I have tested.   See below - which shows 16.04 resolves, 18.04
  and Pop!_OS 19.04 fail, and other distros - Fedora 31, openSUSE Leap
  15.1, and Debian GNU/Linux 10 (buster) - all resolve as expected.

  == Test Case ==
  $ name=$(hostnamectl | grep "Static hostname:" | cut -d: -f2 | xargs)
  $ echo "${name}"
  $ hostnamectl | grep System
  $ hostnamectl | grep Kernel
  $ nmcli dev show | grep DNS
  $ nslookup "${name}"

  == Additional Information ==
  Operating System: Ubuntu 16.04.6 LTS
             Kernel: Linux 4.4.0-170-generic
   IP4.DNS[1]:                             192.168.3.2
   Server:        127.0.1.1
   Address:   127.0.1.1#53
   Name:  BGOWIKI01v
   Address: 192.168.3.60
   ============================================================================
   Operating System: Ubuntu 18.04.3 LTS
              Kernel: Linux 4.15.0-72-generic
   IP4.DNS[1]:                             192.168.3.2
   Server:        127.0.0.53
   Address:   127.0.0.53#53
   ** server can't find BGOWIKI01v: SERVFAIL
   ============================================================================
   Operating System: Pop!_OS 19.04
              Kernel: Linux 5.0.0-21-generic
   IP4.DNS[1]:                             192.168.3.2
   Server:        127.0.0.53
   Address:   127.0.0.53#53
   ** server can't find BGOWIKI01v: SERVFAIL
   ============================================================================
   Operating System: Fedora 31 (Workstation Edition)
              Kernel: Linux 5.3.7-301.fc31.x86_64
   IP4.DNS[1]:                             192.168.3.2
   Server:        192.168.3.2
   Address:   192.168.3.2#53
   Name:  BGOWIKI01v
   Address: 192.168.3.60
   ============================================================================
   Operating System: openSUSE Leap 15.1
              Kernel: Linux 4.12.14-lp151.28.36-default
   IP4.DNS[1]:                             192.168.3.2
   Server:        192.168.3.2
   Address:   192.168.3.2#53
   Name:  BGOWIKI01v
   Address: 192.168.3.60
   ============================================================================
   Operating System: Debian GNU/Linux 10 (buster)
              Kernel: Linux 4.19.0-6-amd64
   IP4.DNS[1]:                             192.168.3.2
   Server:        192.168.3.2
   Address:   192.168.3.2#53
   Name:  BGOWIKI01v
   Address: 192.168.3.60

  ProblemType: Bug
  DistroRelease: Ubuntu 18.04
  Package: dnsutils 1:9.11.3+dfsg-1ubuntu1.11
  ProcVersionSignature: Ubuntu 4.15.0-72.81-generic 4.15.18
  Uname: Linux 4.15.0-72-generic x86_64
  ApportVersion: 2.20.9-0ubuntu7.9
  Architecture: amd64
  CurrentDesktop: MATE
  Date: Sat Feb  8 17:36:28 2020
  InstallationDate: Installed on 2019-12-22 (47 days ago)
  InstallationMedia: Ubuntu-MATE 18.04 LTS "Bionic Beaver" - Release amd64 
(20180426)
  SourcePackage: bind9
  UpgradeStatus: No upgrade log present (probably fresh install)

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