I agree with you in that the focus should be on how long the battery lasts over the % shown on the display. But getting the calibration right to allow a complete charge CAN potentially have an impact on the total charge on the battery.
I can't explain to you all of the behavior of the indicator lights (although I could guess in this case maybe it's that you just used some power when shutting the phone off, so there is some room to "top it off" or something).
However, what I can tell you is the phone doesn't control the battery. The battery itself contains the controller chip that manages it. The battery does not care what your phone's opinion of its current condition is and neither should you.
It may be annoying that you don't have a solid explanation of the indicator light behavior you're witnessing, but they're not an accurate indication of what's happening inside your battery.
If I were you guys, I'd be far more concerned that your actions are actually tricking the battery into an overcharge condition and you're going to wind up killing them in half their normal life expectancy rather than "how long does your battery stay over 95% on the completely inaccurate HTC meter?"
edit: I just realized my reply was to Shadow, but more worded towards the previous message. In response to your specific concern about the meter calibration, two things. First, the meter calibration won't affect how long your battery lasts, only how accurate meter reporting is. Second, if you want to calibrate your meter, constantly topping it off is NOT the way to do it. If anything, this will serve to make your calibration WORSE. If you want to calibrate your meter, you should run your battery until it shuts itself off, then turn it off and full charge it in one sitting (shutting it off so it's not constantly draining during the charge process). This should only need to be done ONCE to calibrate it and doing things like repeatedly topping as being discussed in this thread will HURT that calibration, not help it.

