The hot-key allows you to select the hot-key and possibly a modifier (Ctrl, Alt, ...). If the hot-key is not usable (e.g. it is already grabbed by another application), a warning message-box pops up and the previous hot-key is reset.
Centering timeout specifies a time after the press of the Recenter button and the actual center point registration.
Calibration timeout is a time during which you are supposed to move your head to left/right/top/bottom extremes (that are still usable for the tracking) during calibration. When the time is up, the calibration is finished and the tracking is adjusted appropriately.