With v6, there is also the option to skip those config files all together with below one:
$ pihole-FTL --config misc.dnsmasq_lines
[]
The webGUI settings says this about it:
Additional lines to inject into the generated dnsmasq configuration.
Warning: This is an advanced setting and should only be used with care. Incorrectly formatted or duplicated lines as well as lines conflicting with the automatic configuration of Pi-hole can break the embedded dnsmasq and will stop DNS resolution from working.
Use this option with extra care.