In case you previously have been using custom dnsmasq configuration files with Pi-hole v5, you may want to scrutinise /etc/dnsmasq.d/ as well.
If you want v6 to honor them, you may want to enable misc.dmisc.etc_dnsmasq_d, but note that other processes sometimes write to that directory as well, which may or may not be desired, and which may or may not produce conflicts.
See also Custom dnsmasq configs not loading.