same issue here. in my case it is always set to 1
when I set it to 0 in /etc/my.cnf and reinstall mysql, the value in /etc/my.cnf is set back to 0
when I modify "/www/server/panel/install/mysql.sh" and reinstall mysql, then this file is reverted back to original.
Which means there is no way to set "lower_case_table_names" to 0