Enable comments for post when comments meta box removed

Filter the 'comments_open' check. It happens inside of the function with the same name, and that function is called in a theme usually like this:

comments_open() and comment_form(
    array (
        'comment_notes_after' => ''
    )
);

This is how the filter works:

add_filter( 'comments_open', 'wpse_98775_comment_check', 10, 2 ); 

function wpse_98775_comment_check( $open, $post_id )
{
    if ( $open )
        return $open;

    if ( 'my_post_type' === get_post_type( $post_id ) )
        return TRUE;

    return $open;
}

You could create a custom plugin with this snippet.