paul - Sorry if I'm being pedantic but a point of clarification. Are you (a) departing NRT on an AA-metal flight and/or (b) do you have a stopover at NRT?
AA probably (almost certainly, I would think) can't sell you a ticket HKG-NRT (which is why it doesn't show up). When you say "then again she had no problem with booking me on it" when she booked the through fare to DFW, I assume you are leaving NRT on an AA-metal flight to DFW - correct? If so, do you have a stopover at NRT - perhaps not?
Booking the AA flights HKG-NRT-DFW (no stopover) is not an issue. However, I would be very interested to learn that you could book the AA flight HKG-NRT and then depart NRT on some carrier other than AA and/or have a stopover at NRT (because if you do that, usually the "connection" to the AA-metal flight is lost and you can't book the codeshare HKG-NRT as a result).
No, it is a transit only at NRT and yes I agree that you would have difficulty getitng this flight as an AA# (HKG-NRT) if it was. That said number_6 does imply that it is possible but not easy.