koha-mysql can be used to "provide an interactive mysql shell set up for the specified koha instance". With an option for SQL input, koha-mysql could turn something like this: koha-mysql -e "some sql" instancename into this: mysql --host="$mysqlhost" --user="$mysqluser" --password="$mysqlpass" -e "some sql" "$mysqldb" This might be handy for e.g. updating a syspref in multiple installations.
echo "some sql" | koha-mysql instancename does this. Also good for loading in dumps or whathaveyou.
Ah, yes, I had a hunch there was something I was missing. Marking as resolved/wontfix.