Think of it like this: the annoyance of the microwave telling me my food is done has conditioned me to do what I can to not hear it. It's not about the beep, it's about the response to the beep. When I start clearing the time and entering how long I want to cook I am already agreeing to beeps. Why do that on 2 occasions?
Another way to look at it. Ask yourself, do you have the same habits with a calculator?
Don't know about you, but I subconsciously hit clear on a calculator multiple times before using one but why would I clear the resulting number? Maybe I'm conditioned to operate a microwave like a handheld calculator.
Who needs another clock in the kitchen anyway?