In the /etc/systemd/resolved.conf
Set the DNSStubListener=no like below then restart the network resolvd service this should allow you to run an alternate service on port 53
# This file is part of systemd.
#
# systemd is free software; you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 2.1 of the License, or (at your option)
# any later version.
#
# Entries in this file show the compile time defaults. Local configuration
# should be created by either modifying this file, or by creating "drop-ins" in
# the resolved.conf.d/ subdirectory. The latter is generally recommended.
# Defaults can be restored by simply deleting this file and all drop-ins.
#
# Use 'systemd-analyze cat-config systemd/resolved.conf' to display the full config.
#
# See resolved.conf(5) for details.
[Resolve]
# Some examples of DNS servers which may be used for DNS= and FallbackDNS=:
# Cloudflare: 1.1.1.1#cloudflare-dns.com 1.0.0.1#cloudflare-dns.com 2606:4700:4700::1111#cloudflare-dns.com 2606:4700:4700::1001#cloudflare-dns.com
# Google: 8.8.8.8#dns.google 8.8.4.4#dns.google 2001:4860:4860::8888#dns.google 2001:4860:4860::8844#dns.google
# Quad9: 9.9.9.9#dns.quad9.net 149.112.112.112#dns.quad9.net 2620:fe::fe#dns.quad9.net 2620:fe::9#dns.quad9.net
DNS=127.0.0.1
#FallbackDNS=
#Domains=
#DNSSEC=no
#DNSOverTLS=no
#MulticastDNS=no
#LLMNR=no
#Cache=no-negative
#CacheFromLocalhost=no
DNSStubListener=no
#DNSStubListenerExtra=
#ReadEtcHosts=yes
#ResolveUnicastSingleLabel=no
That wasn't clear from the body, as it says you investigated systemd but hadn't resolved the issue. I'm glad you found a solution though and have a good day.