if you are going to put padlocks or some such on it, it really defeats the the whole idea of an automatic opener. If you hit the opener with it locked in such fashion it could do damage to your door. ( I did that myself one time) There is such a thing as electric solenoid type bolts that work in conjuntion with the auto opener. They pull back instantly when you hit the opener remote.
I would only do the padlock or manual bolting if I was leaving for a trip or something. I also have a sign on my door that says I have an alarm