PHP extension via CLI works but not through apache
So in the end it wasn't an issue with size_t but the size of an integer within their code. There is still mass confusion as to why it works when called by the CLI versus using Apache and a web browser... I may never find out.
What does the apache error_log report? That's almost certainly where you'll find a clue to the cause.
Personally, I'd suspect a permissions problem - remember that the apache user has very limited permissions - certainly more restrictive than yours at the command line.