If you grant an Extra Percentage to any particular affiliate in your Seller Admin > View/Edit Affiliates screen, that extra commission would be calculated on the item subtotal (pre-tax/-shipping) of all sales referred by that affiliate.
Product-specific share percentages do override your Common share percentage for affiliate-referred sales of that product, but this does not affect or override any Extra Percentages, which are calculated separately and in addition to any other affiliate commissions the referring affiliate would normally earn.