This doesn't look like a Pi-hole issue.
I can't really comment on your configuration files, as those is neither one of Pi-hole's nor pihole-FTL's/dnsmasq's files, but rather some Ubiquiti syntax (even if I could, I may have struggled to read it, as you seem to have redacted port and address information from it).
From strictly a DNS point of view, I'd recommend to stick with your Pi-hole to be accessible via IPv4 exclusively - provided your router supports that, which would imply that it allows IPv6 DNS configuration.
The important concept to understand here is that a DNS resolver is fully capable of serving your network of dual-stack (and IPv4-only) clients with IPv6 address information, even if they send their requests only via IPv4.
Any DNS resolver will supply A and AAAA records as requested, i.e. your dual-stack clients are able to resolve public IPv6 addresses from AAAA requests via IPv4.
As mentioned, your router must support configuring IPv6 DNS.
Specifcially, it must not advertise (SLAAC/NDP/RA/RDNSS) or offer (Stateless and Stateful DHCPv6) an IPv6 address as DNS resolver other than Pi-hole, or -as I'd recommend- no such IPv6 address at all.
A router that is not or cannot be configured either way will likely advertise itself or your ISP's DNS servers, allowing clients to completely by-pass Pi-hole via that IPv6 at their own discretion.
Enabling Pi-hole's IPv6 support into that mix would have no effect on your router. It would just lower the probability of IPv6 clients using your router instead of Pi-hole's IPv6 or IPv4 address somewhat.
You should verify the DNS servers your network is aware of, either in your router or on a client, e.g. by running ipconfig /all on a Windows machine and checking the DNS server section.
The reason why I'd recommend to stick with your Pi-hole as only accessible via IPv4 is about associating DNS requests in Pi-hole's Query Log with local hostnames:
With IPv4, clients may (or may not) register a hostname with a DHCP server during DHCP lease negotiation, which in turn may (or may not - some routers don't) populate a co-located DNS resolver with the respective DNS records.
There is no equivalent procedure for IPv6, specifically when auto-configuration is used.
If configured as DHCP server, pihole-FTL/dnsmasq would make an effort to associate IPv6 addresses with hostnames by applying some heuristics, but that's not guarantueed to always work.
Sticking with Pi-hole as IPv4 only will make it easier to identify individual hosts in Pi-hole's Query Log by name.