I’ve always thought that IPv6 has dramatically worse layering than IPv4. In IPv4 over Ethernet, there’s ARP, which layers over plain Ethernet, and IPv4 sits on top of the combination of ARP+Ethernet.
In the IPv6 world, neighbor discovery is IPv6, but only sort of, because the participants don’t necessarily have real addresses. So it’s a mess.
IPv6 link local layers over Ethernet the same way Arp does. Both contain a source/dest MAC which is used for forwarding, both contain the relevant neighbor info. If anything, keeping the protocol's self-discovery messages wrapped in the protocol itself is actually cleaner layering at the cost of complexity (the extra link local signalling addresses).