We would never send a single cut as two pieces unless specifically requested to do so. You don't know what the customer has in mind for the fabric. I've had customers that just wanted to use a long piece for bunting or draping and didn't care what it cost, to buy or to ship.
I don't know how your cart estimates shipping charges, but if it does and if the customer has accepted the estimate, that means they're willing to pay the charges. Trying to save the customer a few bucks on shipping is a noble effort, but not always necessary or even desirable.
We also won't overpack flat rate envelopes, the PO has every right to refuse them, or to send them back.