Another thread got me wondering about this. 702.3 says, except as modified by this article, all applicable articles of this code shall apply. So, would this negate using a GenTran style transfer panel for emergency power of circuits that are AFCI protected, since this would seem to bypass this protection when transferred to generator power? This would also seem to be the same situation for circuits normally protected by a GFCI circuit breaker.
IMO, if you put those circuits on the Gen Tran panel, then you would be bypassing the required protection and that would be a code violation. Two ways to avoid this that I can think of for an existing wiring system, install a transfer switch ahead of the panelboard or use the InterLockKit system.
Few things are harder to put up with than the annoyance of a good example.