In general, you should avoid using a GUA address for Pi-hole.
Pi-hole needs a fixed IP, and with a GUA IPv6, the prefix as well as the interface identifier are likely to change.
By default, Docker is IPv4 only.
If you want IPv6 for a container, you'd have to enable that for Docker's daemon in general as well as for a specific container.
Your observation would suggest that communication between your host OS, the Docker daemon and the container isn't frictionless.
Also note that Docker's IPv6 support could have been breaking network isolation in the past.
It seems Docker tried to address this in the meantime, but it may yet be considered experimental, as explicity allowing some experimental features is recommended by Docker, see Enable IPv6 support | Docker Docs.
But I would recommend to forego IPv6 for Docker altogether.
Your debug log shows you are using a FritzBox router.
Those routers support configuration of distributing an IPv4 DNS server exclusively, while not advertising a DNS server's IPv6 address at all, see e.g. Unresolved ipv6 adress in my top list - #4 by Bucking_Horn.
This would have clients send their DNS requests via IPv4 exclusively, while Pi-hole would still answer any allowed request for an AAAA record with a set of IPv6 addresses, so dual-stack clients would retain their full IPv6 resolution capabilities.