Currently the NetBSD IPv6 stack, when acting as a router and forwarding
  traffic, treats any packet with a Router Alert hop-by-hop option as
  'ours' and sends it to the local stack. This stops the packet from
  being forwarded any further, and also results in ICMPv6 Destination
  Unreachable message being sent back.

That's definitely broken.

My understanding, which may be a bit off, is that router alert is
essentially a method to enable routers to skip a whole bunch of checks
that may be costly when the option is *not* present.

Do you know if MLD packets would be handled properly if there were no
router alert special treatment?

I would be inclined to commit a version of the FreeBSD patch (the one I
looked at since you listed it first).  Are you set up to prepare and
test such a patch on NetBSD-current?