Another option is to add another second IP address (IP aliasing) to the network interface:
If you bind the daemons (pihole-FTL, named from Bind9 etc) to the appropriate interfaces you can have two DNS servers running on the default port 53 but listening on different IP's.
Same can be done if for example you want to run another web daemon (nginx, apache2 etc) alongside Pi-hole's lighttpd daemon.