the value in the invoice is showing is the total order quantity but not the supply quantity.
If you are creating Pro Forma invoice with ref to Order( F5) system obviously copies the sales order qty the control is in VTFA ( the field billing qty C) controls. I assume you are creating Pro Forma invoice with ref to Sales order and this is standard behaviour only.
And if you create Pro Forma invoice (F8) with ref to Delivery then system copies the delivery qty only not order qty, here the control is in VTFL the field billing qty is D ( delivery qty).
So in your case if you want to create the Pro Forma invoice for the delivered qty you can create the Pro Forma invoice with ref to delivery and please note here you need not do any PGI for creating Delivery related Pro forma invoice.After creating Pro Forma invoice also you can do PGI.