Your best option at this point is to use FTLDNS beta.
I think because your environment already has an embedded dnsmasq, it will cause a lot of headaches trying to isolate the issue with it.
FTLDNS beta does not need dnsmasq to work any longer.
You would most likely have to disable dnsmasq from running so that FTLDNS can take over port 53.
The installer WILL fail at starting DNS. It is to be expected since dnsmasq is active and using port 53.
After install, I recommend editing /etc/systemd/resolved.conf and un-commenting DNSStubListener=yes and change it to DNSStubListener=no
then run sudo systemctl restart systemd-resolved.
This should release port 53 and you'd be able at this point to start pihole-FTL as your DNS resolver with
sudo systemctl start pihole-FTL.service