Hello Debayan,
I implemented this scenario last year with three North american companies, so I know the scenario quite well. I think Julie Phan is correct with her answer, if only FI reconciliation is the issue.
Think about what happens, when the freigt invoice is captured in Financial Accounting. If your SD freight condition is a proper accrual condition (which I assume), the posting is $100 freight accrual account against freight expense account. The $100 was not posted on cost center, but on a COPA profitablity segment (as desired). So for the $150 freight invoice, $100 can be matched in a first line item against the open accrual line item, while $50 still need to be expensed in a second line item. If you expense the $50 against a cost center, Accounting might be happy (freight invoice is successfully posted), but you loose the context of the sales order/delivery with the cost center assessment. In this situation I would recommend to assign the $50 to the correct COPA profitability segment by adding the sales order (position) in the posting block of the second line item. SAP can then derive all the characteristics by itself. You have to adjust the field status group of the freight expense account to work properly.
This whole procedure is extra work for Accounting though. It depends on whether the freight expense deviations warrant the extra effort. I implemented the solution as described, but 2 out of 3 companies decided later it was not worth the extra effort and returned to simple cost center expensing, which is Julie's solution.
Regards,
Steffen