"set names" vs mysqli_set_charset — besides affecting mysqli_escape_string, are they identical?

It seems to be common knowledge to use mysql_set_charset / mysqli::set_charset instead of the direct MySQL query set names.

The reason often cited is that set names is insecure because the encoding used for mysql_real_escape_string / mysqli::real_escape_string will only be set by a call to mysql_set_charset / mysqli::set_charset. (Another reason cited is that the PHP docs says it's "not recommended" §.)

However, is it safe to use the direct MySQL query set names if we use prepared statements andor other means of escaping besides mysql_real_escape_string / mysqli::real_escape_string / mysqli_escape_string?

Besides affecting the encoding of mysql_real_escape_string / mysqli::real_escape_string / mysqli_escape_string, Is there any difference between set names vs mysql_set_charset/mysqli::set_charset?