Starting with 6.0, the “dnsmasq.d” setting is disabled by default
pihole.toml says:
# Should FTL load additional dnsmasq configuration files from /etc/dnsmasq.d/?
etc_dnsmasq_d = false
Source: Etc/dnsmasq.d files
Set the parameter “etc_dnsmasq_d" in the “pihole.toml” to true and it will work in Pi-hole 6.0 too.