Avez-vous essayé de transmettre l'expression entière comme valeur de liaison ?
$sql = 'INSERT INTO '.POLYGON_TABLE.' (user_id, polygon, polygon_type) VALUES (:userId, PolygonFromText(:polygonArea), :polygonType)';
$sth = $this->pdo->prepare($sql);
$area = sprintf("POLYGON((%s))", $polygon->getPolygonAsText());
$sth->bindValue(':userId', $polygon->getUserId(), \PDO::PARAM_INT);
$sth->bindValue(':polygonArea', $area, \PDO::PARAM_STR);
$sth->bindValue(':polygonType', $polygon->getPolygonType(), \PDO::PARAM_STR);