I agree that the duplicate info messages in /var/log/messages are annoying. I think that the loglevel going to 'journal' should match what goes to 'console'. The default configuration uses a loglevel of WARN for 'console'.
Editing /etc/matrix-synapse/log.yaml to add "level: WARN" in the 'journal' section of 'handlers' seems to do the trick. Important warnings should still show up in /var/log/messages, but all of the info stuff should only go into homeserver.log. It would be nice if debian shipped it this way as well.
