You can add a labels: stanza to your app.yml to include docker labels on the discourse container when it is started by launcher. Alternately, you can use ./launcher start-command app to see the docker start command and then use whatever you want to use those same ENV variables to start the Discourse container.
You don’t say what Watchtower wants or needs to exclude Discourser from Watchtower, so I can’t tell you any more.