Is MB_DB_CONNECTION_URI used?

Both https://github.com/metabase/metabase/blob/master/bin/start and https://github.com/metabase/metabase-deploy/blob/master/bin/start set

export MB_DB_CONNECTION_URI="$DATABASE_URL"

Is this actually used anywhere? It seems like only the variables set in MB_DB_* are used for the DB connection

Yes, you can use MB_DB_CONNECTION_URI or the individual MB_DB_* environment variables, either works.

That line in particular is used on Heroku, which provides the application database URL as DATABASE_URL.