Support for multiple subnets/local domains/DHCP servers

I could not follow what you wish for exactly. Are you are looking for more than one conditional forwarding field in the GUI? This is already in the pipeline

Also note: pihole uses dnsmasq internally and can use its config files. So everything you can do with dnsmasq you can also do with pihole. You just have to manually create config files in /etc/dnsmasq.d/ and restart pihole.