You should not need to change the typemap. The following works:
<?php
$manager = new \MongoDB\Driver\Manager;
$query = new \MongoDB\Driver\Query( [] );
$cursor = $manager->executeQuery( 'dramio.checkins', $query );
$cursor->setTypeMap( ['root' => 'array', 'document' => 'array'] );
$results = $cursor->toArray();
echo hexdec(substr((string) $results[0]['_id'], 0, 8)), "\n";
?>
(outputs "1452730554").