TL;DR: Essentially because of some quirk with networkd, all interfaces get stuck in a '(configuring)' state forever unless you set an empty link-local address for at least the primary interface (but I set it for both).
Systemd-network-wait-online.service waits for at least one interface to be fully online, and won't consider an interface to be fully online if it's in '(configuring)' status when you run networkctl status some-iface
.
Set link-local: []
to be set on every interface: