There are still a few possibilities for how it could work— first would be running multiple instances of dnsmasq and then putting a reverse proxy in front of them that would direct the traffic based on who's asking.
Another would be switching to a purpose-built DNS resolver/cache that had this capability.
Finally, you could have per-client DNS IPs, but this would require the cooperation of the DHCP server, which is less typical on a home network where that's often a closed-source router. But a "super pi-hole" following this pattern could also potentially be the DHCP server. (Yes, raspberry pi can run OpenWRT: https://openwrt.org/toh/raspberry_pi_foundation/raspberry_pi)