Ordering of mysql_upgrade tasks is not optimal

When upgrading MariaDB 5.5.31 to MariaDB 10.0.12, because of the order that mysql_upgrade performs the upgrade of the 'mysql' tables, one can see many errors like the following:

2014-08-05 13:22:49 7ec848562700 InnoDB: Error: Fetch of persistent statistics requested for table "dbname"."table1" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2014-08-05 13:22:49 7ec848562700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
...

It does this for each and every table being checked.

MySQL/Oracle supposedly fixed this in their mysqlcheck/mysql_upgrade:

http://bugs.mysql.com/bug.php?id=68163

However, I am unable to run mysql_upgrade with the --skip-database option without receiving an error. I've added the "loose" prefix as well, but it doesn't seem to change anything.