In terms of getting a credit versus a cash refund It shouldn't matter at all what the rebooking options were. If it did then AA would seemingly deny any refund at all (even the credit) on the grounds that a rebooking option was offered.

When flights have been majorly disrupted I've never had an issue getting partial refunds for partially flown itineraries, it seems that in this case someone at AA just issued the wrong refund type. I would try submitting another refund request with the new credit number, not sure what else to do.