Hi Alejandro,
if the active display area is only slightly wrong you probably won’t notice. But if it’s totally off when you’re trying to calibrate, then the calibration probably won’t succeed, and/or the tracking accuracy will be sensitive to head movements.
The benefit of separating display area setup and user calibration is that it allows for a larger track box: that is, the user may move her head freely and still get good gaze accuracy.
You don’t have to set the display area all the time unless you move the tracker or the screen. The tracker remembers the last setting. (Except if you run the EyeX Engine in between, because it sets the display area to what it thinks it should be.)