Resolved: I edited /etc/dnsmasq.conf to make the listening port 5353, restarted pihole-FTL and that removed the error. I then changed it back to port 53, restarted again and now it's working fine.
That would imply that some dnsmasq process is still running on your machine.
You could verify that, e.g. with sudo ss -tulpn sport = 53.
If you didn't stop and disable dnsmasq, that may have left the already running instance intact.
You may want to scrutinise your /etc/dnsmasq.conf as well, as that file usually only points to the configuration directory, i.e. it does not contain any port information.
And if some other dnsmasq would still be present, it's likely that your edit may only be a temporary fix, and the issue will be reintroduced by one of the next reboots.
In any case, applying jfb's advice is the correct way to address the issue of dnsmasq conflicting with Pi-hole (provided you are not depending on dnsmasq for other reasons).