The documentation doesn't explicitly state that the file name for the custom query should end with .sql:
https://www.zabbix.com/documentation/current/en/manual/config/items/itemtypes/zabbix_agent/zabbix_agent2#mysql.custom.query
Which is confusing.
The plugin documentation explains this better:
https://git.zabbix.com/projects/ZBX/repos/zabbix/browse/src/go/plugins/mysql/README.md?at=refs%2Fheads%2Frelease%2F7.0
I think we should add more details from the plugin documentation or at least a link to it.