Dear Mr. Ankit,
When you had purchased the raw material for manufacturing the goods from the vendor you were on the second stage biller. And once you have manufactured the goods any waste, scrap or runner going out of the unit will be treated as first stage billing since the tax source generation will be starting from you. The major reason being, the item (raw material) purchased by you has ended by the taxes you have paid to the supplier you purchased from therefore the billing stage has ended. Now the new generation will start from you as it is a waste of the manufacturing unit.
As far the naration is concerned, it depends from item to item and commodity to commodity. Yes this is true the duty that has to be passed on will be as per the original excise invoice you have recived from your supplier from where you have purchased the raw material because you are not making any profit/loss out of those goods. You are just clearing the debt stocks and clearing the inventry.
For final conclusion, I strongly suggest you to constant the C/A as the excise matter is not that simple as we usually feel.
Thank you!
Regards,
Krunal Parekh