They were probably configured by one of the fancy network config daemons (systemd-networkd, dhcpcd or similar). They like to take over RA processing, and they add IPs with "noprefixroute" so they can add the route themselves separately.
RAs have nothing to do with link-locals, but I bet one or the other of those daemons also takes over configuring link-local addresses and does the same thing there. If you looked in the routing table, there'll be a prefix route for fe80::/64 that was added by the daemon.
This wouldn't affect how DNS replies are sorted though. On machines without non-link-local v6, AAAA records aren't handled by trying them first and then expecting them to quickly fail. They're handled by pushing them to the bottom of the list so that the A records are tried first.