Some STDERR output was handled by LSAPI's STDERR stream, some written to file handle 2 (stderr). stderr log is for the later case. However, LSAPI STDERR stream is always written to error log. The warning from PHP is handled by LSAPI STDERR not stderr file handle. Hence what you see.
To suppress PHP Warning, you should change php.ini. So no warning from PHP gets sent to LSAPI STDERR.