In general, you should edit /etc/pihole/pihole.toml.
The post linked above is for a very specific case where an existing automated ansible script creates a custom.list containing enriched contents along with comments that wouldn't carry over easily otherwise.
The solution I proposed allows to continue using that file as produced right now, without needing to adjust the existing ansible workflow.
If your use case isn't that, then stick with editing pihole.toml.
Pretty much yes, as pihole.toml combines various settings previously strewn over different config files in v5 (like setupVars.conf, pihole-FTL.conf and /etc/dnsmasq.d/*).