I have been meditating for a couple of years now. Far from a Zen expert but I do relax enough to get refreshed from my sessions. To answer your question, during calibration I follow the instructions and relax. I concentrate on my breathe (I usually don't do this when I meditate unless I'm more stressed out that usual) because the instructions tell me to. I relax and instead of trying to blank my mind I let it do what it wants (per instructions) but I am in a fairly relaxed state at this point.
During the actual session I do what I do when I meditate. Sometimes I'll do breathe, sometimes a partial body scan but usually I most enjoy trying to do and think of absolutely nothing. While I can feel underlying stress (if having stress) but in my conscious I can stay mostly in a "blank, clear" state. Gently pushing thoughts out.
I know I am stressed inside so maybe Muse is catching it. But as I mentioned in my post I recall from many years ago having stress (and depression) deep inside but achieving a very relaxed state as demonstrated by the flat line of lights. With Muse I am unable to get to that point.
So...I hope that helps you help me but...all my post was really requesting was different users opinion on the data reliability. And you didn't even offer yours;)