It looks like a /128 prefix length is not permitted on an interface, according to draft-ietf-ipv6-addr-arch-v4-04.txt, which I think means most of the issues I was concerned about described disappear.
I'm still not sure exactly how host routing would work from the end-nodes point of view, so I'll continue to do some reading. It seems to me that hiding the network or subnet topology by not grouping IPv6 addresses according to their common data links means that the subnet bit portion of the address loses its significance when determining whether a destination address is off or onlink, during Neighbour Discovery.
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