Hmmm, that is interesting, and I'm sorry to hear that! I probably wouldn't have rung AMEX, as what you are trying to do is clearly excluded by their T&C's (despite a large number of people, myself included, having no problems getting the points) and I wouldn't want to bring that to their attention. That aside though, I think I would let the application proceed, as you've got nothing to lose at this point - assuming AMEX are still offering pro-rata refunds in Oz - which I certainly believe they still are. Others may be able to correct me on this, or confirm.
If the points come through, then great, if they don't, call and cancel asking for an annual fee refund. You could always try negotiating for the points, but I wouldn't hold out much hope if they don't credit automatically. I would have used the reason that the bonus points didn't come through as expected, but they have probably logged your call about that on file already. Either way I think you'll get an annual fee refund if you need it - assuming you don't use the $300 travel credit etc.
Post back and let us know how you go. I'm sure others will be very interested. I'll be apply for another AMEX card this week, and I'll let the team know if the points don't post.
Yeah, kind of a bummer.
I did ask the question of refunds a few months back, I understand they don't do pro-rata refunds but if it is early in the piece and you haven't obtained any benefits (e.g., points, flight redemptions...etc), you can ask for a cancellation and the annual fee should be reversed.
I'll see what happens after the card arrives. It is what it is. Haha.