Custom PDF template in Commerce Billy
This table is actually the rendered view 'Line items (Commerce Line Item)' which is created in code by Drupal Commerce. So all you have to do is to modify this view to your needs.

To further customize the display of your invoice, you can make a copy of css/pdf.css and themes/commerce_order--commerce_order--pdf.tpl.php located in commerce_billy_pdf folder into your custom theme and experiment.