gtid_slave_pos, innodb_table_stats, innodb_index_stats missing after upgrade

Upgraded from MySQL 5.5.13 (SLES 11.3) to MariaDB-10.0.9. At first I missed migrating configuration to the new install and XtraDB engine did not find tables presumably because tablespace is on different filesystem/path with innodb_file_per_table. After I put in correct configuration I got following problems even following re-running mysql_upgrade --force:

Repairing tables

mysql.gtid_slave_pos

Error    : Table 'mysql.gtid_slave_pos' doesn't exist in engine

status   : Operation failed

mysql.innodb_index_stats

Error    : Table 'mysql.innodb_index_stats' doesn't exist in engine

status   : Operation failed

mysql.innodb_table_stats

Error    : Table 'mysql.innodb_table_stats' doesn't exist in engine

status   : Operation failed

Phase 3/3: Running 'mysql_fix_privilege_tables'...

Replication (slave) also complains about this, but keeps going nonetheless. I had no problems upgrading an identical server without InnoDB, so my guess is the new tables were added to the shared tablespace in MySQL datadir, which I am not using. This is presumably "user error", however, mysql_upgrade --force should re-create them, unless there is another easy way to do so.