Post-fix:
Reverting the patch for MDEV-6069 brought some ALTERs with
ENGINE=MYISAM back into the mysql_system_tables_fix.sql
script. As a result, running mysql_upgrade with global
enforce_storage_engine=INNODB (or any other non-MyISAM
engine, for that matter) would fail.

Fixed by locally unsetting enforce_storage_engine in the
upgrade script.