There are still suppressions in MTR files which reference MySQL. Possibly many of those suppressions aren't needed at all, but removing them should a separate task. Meanwhile they need to be synchronized with the error messages, as some of them can be there to prevent irrelevant sporadic failures (and thus might not show up in test results right away).

./suite/galera_sr/r/galera_sr_mysqldump_sst.result:CALL mtr.add_suppression("Slave SQL: Error 'The MySQL server is running with the --skip-grant-tables option so it cannot execute this statement' on query");

include/mtr_warnings.sql: (": The MySQL server is running with the --secure-backup-file-priv option so it cannot execute this statement"),