A solução foi super simples: examine as variáveis e tente localizar as relevantes:
log_timestamps | UTC
Então eu mudei para 'SYSTEM':
mysql> SET GLOBAL log_timestamps = 'SYSTEM';
# /var/log/mysql/mysql_queries.log
2016-02-24T18:54:23.837289Z 2 Query SET GLOBAL log_timestamps = 'SYSTEM'
2016-02-24T10:54:25.949232-08:00 2 Query show variables
O tempo no registro alternou de 18:54 a 10:54 como deveria.
- log_timestamps
This variable controls the timestamp time zone of error log messages, and of general query log and slow query log messages written to files. It does not affect the time zone of general query log and slow query log messages written to tables (mysql.general_log, mysql.slow_log). Rows retrieved from those tables can be converted from the local system time zone to any desired time zone with CONVERT_TZ() or by setting the session time_zone system variable.