But by being pro-active, as you are, you greatly increase the odds of getting a stove on board. And you do exactly what I would do: call ahead of time (and get name of person who says "OK!"); keep the fuel bottle clean (the soap is a nice touch); and have it in hand or very handy at the counter so the baggage clerks can see what it is and feel at ease. And, as you note, all of this may go for naught.
We've had another suggestion on the Gear Guy Forumthat you mail the stove ahead of time via UPS ground or some other shipping service. That can work, too, but may necessitate some fooling around on the pickup end. I'd suggest as well that if you know that butane/propane canisters are available at your destination, you simply purchase an inexpensive stove such as the Gaz Twister HPZ ($30). Without a canister attached, this stove looks pretty innocuous, and even if it gets confiscated, the loss is not large.
If anybody else out there has had some illuminating experience with this issue in recent months, please share your wisdom in the Gear Guy Forum!