Would be nicer if systemd-networkd supported multiple prefixes directly
I believe a fix for this was merged last year please read https://github.com/systemd/systemd/issues/22571 and https://github.com/systemd/systemd/pull/22574. Check what version it was actually released and if your Linux latest version already has it.
Another option would be to create a bridge and/or macvlan and them place multiple virtual connections on it, each one requesting and having a different IPv6 prefix.