I think that mechanical key behaviour depends on the car. I'm pretty sure my BMW sets off the alarm if I use the mechanical backup key, but it turns off when I put the key in the ignition slot.
(One day, when I can be arsed, I'll rekey the car and reprogram it with fresh transponders, but today is not that day!)
But "reprogramming" a key (more like adding a key) on that model of ford just involves doing a dance with the fob key then inserting the key with the new transponder. So we plan to get all keys working on the car at some point. I was just going to order a new chip but my bother was complaining about the key barrel being a bit loose on him so just doing to replace everything at some point. Its just more about not being lazy about it :-P
Thing is, its what we call "the work horse" car of the family, it gets used about once a week to do tasks no one wants to do in their own cars (or when I need to do something in a car), so its not really a high priority thing to fix, but if we are going fix it might as well do it "right")