Right, I understand why it would be needed in a ping. But since the DNS
server config in systemd-resolved applies to a specific link, the scope
ID is implied.

As far as your desktop vs server systems, maybe it's the difference
between the interfaces available on each system? If you only have one
non-lo interface on the server, the scope ID shouldn't be necessary. But
if your desktop has e.g. both wlan0 and eth0, then I would expect you
need to specify the scope ID in a ping.

My system is working with systemd-resolved in stub mode, using my DNS
server's IPv6 link-local address. So maybe there is something else on
your system causing the problem.

Is there anything else odd about your network configuration? Can you
share the output of `systemd-analyze cat-config systemd/resolved.conf`?
Also when you are in stub mode, what does `SYSTEMD_LOG_LEVEL=debug
resolvectl query google.com` show? It may be a good idea to run
`resolvectl flush-caches` after switching back to stub mode.

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https://bugs.launchpad.net/bugs/2003778

Title:
  systemd-resolved uses malformed link-local IPv6 forwarder

Status in systemd package in Ubuntu:
  Incomplete

Bug description:
  In a network with a local nameserver that has IPv4-address 10.1.0.1
  and link-local IPv6-address fe80::2a0:57ff:fe24:b041%2 'resolvectl'
  returns:

  Global
         Protocols: -LLMNR -mDNS -DNSOverTLS DNSSEC=no/unsupported
  resolv.conf mode: uplink

  Link 2 (ens33)
      Current Scopes: DNS
           Protocols: +DefaultRoute +LLMNR -mDNS -DNSOverTLS 
DNSSEC=no/unsupported
  Current DNS Server: fe80::2a0:57ff:fe24:b041
         DNS Servers: 10.1.0.1 fe80::2a0:57ff:fe24:b041%21905
          DNS Domain: < edited >

  Name resolution fails because the indicated 'Current DNS Server'
  IPv6-address is an incomplete link-local address. Also the link-local
  IPv6-address indicated in the second position of the 'DNS Servers'
  line is malformed. Issuing consecutive 'resolvectl' calls have the
  last 4 digits in this line changing, i.e. they all show
  'fe80::2a0:57ff:fe24:b041%2', which would be the correct link-local
  IPv6-address including the interface specification, but then 4 digits
  that are not constant.

  Workaround:

  Take systemd-resoved out of stub-mode with:

  (cd /etc && sudo rm -f resolv.conf && sudo ln -s
  /run/systemd/resolve/resolv.conf resolv.conf)

  The auto generate file '/run/systemd/resolve/resolv.conf' has the
  proper specification of the name servers link-local IPv6-address:

  nameserver 10.1.0.1
  nameserver fe80::2a0:57ff:fe24:b041%2
  search < edited >

  The broken stub mode is configured with:

  (cd /etc && rm -f resolv.conf && ln -s /run/systemd/resolve/stub-
  resolv.conf resolv.conf)

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