How do I alter the comment form ‘allowed tags’ text in a plugin?

Here you go… Use this code:

<?php
add_filter('comment_form_defaults', 'change_allowed_fields');

function change_allowed_fields($defaults) 
{
    //All the comment form fields are available in the $defaults array
    $defaults['comment_notes_after'] = "<b>Markdown for the win!</b>";

    return $defaults;
}

This will work!