Just did a quick test on ubuntu:
installed mysql-server, which created /etc/mysql/my.cnf
mysqld --verbose --help | grep -A 1 "Default options"
110112 13:35:26 [Note] Plugin 'FEDERATED' is disabled.
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf /usr/etc/my.cnf ~/.my.cnf
created /etc/my.cnf and /usr/etc/my.cnf, each with a different port number
restarted mysql - it was using the port number set in /usr/etc/my.cnf
Also meanwhile found the --defaults-file option to the mysqld. If you specify a config file there, only that one will be used, regardless of what is returned by /usr/sbin/mysqld --verbose --help | grep -A 1 "Default options"