I'm confused by the direction of the pipes. Most of the examples in this documentation opens pipe #2 as "r", because they want to read from stderr. That sounds logical to me, and that's what I tried to do. That didn't work, though. When I changed it to w, as in
<?php
        $descriptorspec = array(
           0 => array("pipe", "r"), // stdin
           1 => array("pipe", "w"), // stdout
           2 => array("pipe", "w") // stderr
        );
        
        $process = proc_open(escapeshellarg($scriptFile), $descriptorspec, $pipes, $this->wd);
...
        while (!feof($pipes[1])) {
            foreach($pipes as $key =>$pipe) {
                $line = fread($pipe, 128);
                if($line) {
                    print($line);
                    $this->log($line);
                }
            }
            sleep(0.5);
        }
...
?>

everything works fine.