That's wrong, mDNS does not bind to the loopback address or link-local addresses, nor any unicast address at all.
Since DNS and mDNS are separate protocols, there is no conflict here.
DNS is unicast to port 53, while mDNS uses port 5353 on multicast addresses.
And DNS may well return a name for loopback addresses, just as mDNS may return an IPv6 GUA for some hostname.local.
Assuming you meant to write FTL instead of FTP 
, this would be possible already.
As a tailored fork of dnsmasq, pihole-FTL would allow you to exercise exact control of its binding and listening behaviour as detailed by dnsmasq documentation, see specifically its interface, listen-address and bind-interfaces options (among others).
To apply them, you'd need to configure Pi-hole to not manage interface listening behaviour at all, by switching dns.listeningMode to NONE, under All settings » DNS server .
You could then add your desired custom configuration to Pi-hole.
For just a few lines, you could use misc.dnsmasq_lines under All settings » Miscellaneous.
If instead you want to manage your own custom dnsmasq file under /etc/dnsmasq.d/, you could alternatively enable misc.etc_dnsmasq_d.
All settings is available in Expert mode only.
A side note on shutting down DHCP for your network:
You should be aware that NDP/SLAAC does not register hostnames with DNS, i.e. in an IPv6-only network, without DHCP based hostname registration, you would see only IPv6 addresses as Client in Pi-hole's Query Log (or generic public domains, perhaps).