The third parameter is somewhat confusingly named; it would probably be better described as "$set_state". If true, it sets the bit to 1. If false, it sets the bit to 0. Default is true.
<?php
$num = gmp_init(1);
gmp_setbit($num, 1);
echo 'gmp_setbit(1, 1): '.gmp_strval($num, 2)."\n"; // 11
$num = gmp_init(1);
gmp_setbit($num, 1, true);
echo 'gmp_setbit(1, 1, true): '.gmp_strval($num, 2)."\n"; // 11
$num = gmp_init(1);
gmp_setbit($num, 0, false);
echo 'gmp_setbit(1, 0, false): '.gmp_strval($num, 2)."\n"; // 0
?>