This function DOES return TRUE if the key has a passphrase, you just need to set up the data in such a way that the function can understand it. It is not documented here.
This error message led me to the solution:
PHP Warning: openssl_x509_check_private_key(): key array must be of the form array(0 => key, 1 => phrase)
So this works:
$certFile = file_get_contents('cert.crt');
$keyFile = file_get_contents('cert.key');
$keyPassphrase = "password1234";
$keyCheckData = array(0=>$keyFile,1=>$keyPassphrase);
$result = openssl_x509_check_private_key($certFile,$keyCheckData);
