I know in the past two years approximately 9 people including myself who did AOA internships and went on to radiology, anesthesiology, and pm&r without any difficulty. In one case, the person emailed the ABR specifically and they approved his intern year in writing. I can't see how they would allow you to go into ACGME residencies such as Cleveland Clinic, Johns Hopkins, and Emory as 3 of the 9 people did in different fields and not board certify you later. It's my understanding that AOA years count and since you are doing an ACGME residency then they will allow you to be board certified just like all the others. Not to mention with the merger programs have been applying for pre-accreditation and are technically under the ACGME umbrella now.
If concerned, then just email the ABR. Last year I remember the website saying AOA year as well as ACGME or RCPSC. They may have just updated their website because with the merger the AOA designation is technically going away.