I'm not a tk wizard by any means. Chapter 14 in Mastering perl/Tk describes how to subclass widgets, which might allow you to add the space you want.

Another possibility (and I'm open to correction on this) might be to write a subroutine that launches your message box, allowing you to automatically add the space you're looking for. Maybe something like this:

#!/usr/bin/perl 
use strict;
use warnings;
use Tk;

my $mw = MainWindow -> new;
my $result = messengerBox ('question', 'Hello World etc', 'PopUpBox', 
+'AbortRetryIgnore', 'Retry' );

print STDERR "$result\n";

MainLoop;

sub messengerBox
    {
        my $icon = $_[0];
        my $message = $_[1];
        my $title = $_[2];
        my $type = $_[3];
        my $default = $_[4];

        $message = '   Add the space here    ' . "$message";

        my $response = $mw->messageBox(-icon => $icon, -message => $me
+ssage, -title => $title, -type => $type, -default => $default);
        return $response;
    }
[download]

But I guess a mega-widget would be the preferred method.

I hope that's of some help.