Please note that ZIP archives do not support unicode encodings like UTF-8, so multi-byte characters cannot be shown in standard ZIP viewers like WinRAR or 7-zip. However, the text will stored as-is, so it is at least possible to display UTF-8 comments in your own desktop or web applications. If you want to test with PHP and output in a browser, don't forget to set page charset to UTF-8 too:

header("Content-Type: text/plain; charset=utf-8");

Zip archives are encoded in ISO-8859-1 when stored but comments seem to be added in UTF-8 everytime. So...

<?php
   $zip->setArchiveComment("Peña");    //outputs "Peña" as the comment.

   $zip->setArchiveComment("Peña");    //outputs "NULL" as the comment / no comment is displayed.
?>

Using mb_internal_encoding() or mb_http_output() wont change this behavior.
At the end you can fix your corrupted comment using something like str_replace();

Consider this:

<?php
$zip = new ZipArchive;
$res = $zip->open('test.zip', ZipArchive::CREATE);
if ($res === TRUE) {
    $zip->addFromString('test.txt', 'file content goes here');
    $zip->setArchiveComment('Peña'); //outputs "Peña" as the comment.
    $zip->close();
    $file = file_get_contents('test.zip');
    file_put_contents('test.zip', str_replace("Peña", utf8_decode("Peña"), $file)); //outputs "Peña" as the comment. FIXED!

    echo 'ok';
} else {
    echo 'failed';
}
?>

ZipArchive (using libzip) encodes comments in UTF-8/ASCII, but some softwares on Windows show comments in ANSI (such as GBK...), so we should :

<?php
    $_charset = 'GBK';
    $file = 'D:/boaphp.zip';
    $comment = '中文ABC123';
    
    $zip = new ZipArchive;
    $res = $zip->open($file, ZipArchive::CREATE);
    if ($res) {
        //add files here

        if($_charset){ //for Winrar, 7z...
            $zip->close();
            
            $str = mb_convert_encoding($comment, $_charset, 'UTF-8');
            $fh = fopen($file, 'r+b');
            fseek($fh, -2, SEEK_END);
            $str = pack('v', strlen($str)) . $str;
            fwrite($fh, $str);
            fclose($fh);
        }else{ //for PHP: $zip->getArchiveComment()
            $zip->setArchiveComment($comment);
            $zip->close();
        }
    }
?>