Hi Jamal,
I am pretty sure Alternative Reconciliation functionality is only with finance related postings to customers, vendors and assets such as transaction FB60, FB70, FB01, FB02 and FB05. It can not be used with the document entry transaction that are linked to other components such as MIRO (Logistic Invoice Verification) or VF01 (create billing document).
Ajay, please correct me if I am wrong.
Thanks
Naseem