DNS resolution on LLA address fails

Pi-hole isn't involved here: It is the respective OS's IPv6 addressing that would or would not require a scope id, despite expectations of working without one.
You should also note that the scope id is specific to the client, so on your MacOS machine, you'd have to use that machine's interface that handles communication to your Pi-hole machine, which may well have a name different of eth0.

But as you mention you'd want to use this in a Fritzbox router:

Your FB does not have to advertise any IPv6 address as DNS server.
It already distributes an IPv4 address via DHCP, so your IPv4 only as well as your dual stack clients will already know a DNS server - and one DNS server is fully sufficient.

Just configure your Fritzbox to not distribute an IPv6 address as DNS server at all, see e.g. Unresolved ipv6 adress in my top list - #4 by Bucking_Horn.

That configuration not only avoids using an LLA altogether, it also makes Pi-hole's Query Log less cluttered and easier to read.