The problem with Docker is that assumptions of NAT and proxies are built-in quite deeply into the v4 networking functionality and defaults. With v4 it just exposes NATed rfc1918 space subnets to containers with a hardcoded prefix that's by default the same for all Docker installations in the world.

The sensible way to use it in the ipv6 world would be to give Docker its own globally routable prefix(es) acquired via eg dhcpv6 prefix delegation. The current manual prefix configuration is not how things should work in v6.