甲方為交付乙方產品而耗用的包裝，輔料，運輸及保險等項開支 = extra expenses

加工 in '在加工以外收取' is actually 加工费 = processsing fee

I guess "每套合同產品" in 但這些費用不超過每套合同產品的 ( ) % means 'price/cost per contract product', where 合同產品 = contract product, or product based on or under or in or as described the contract.

So the structure of this sentence is:
The 'extra expenses' shall be gathered in addition to the 'processing fee', but 'these expenses' shall not exceed ()% of the 'price/cost per contract product'.