Hi Julian!
Simply if your chip has a defect hot Pixel on Location x,y 1,1
The hot Pixel will be on all Images, dark, bias, light(!!!!) on position x,y 1,1 no matter how you turn your camera around.
Calibration therefore will correct all these pixels
For the lights the sky will turn 180 degree after flip mount, but this turn on the image is recognized by the Star Alignement Prozess and rotated back correctly,
BUT AFTER the calibration (with bias, dark,flat)!!
So your hot Pixel at 1,1 will be removed by Calibration and afterwards StarAlign rotates the calibratet lights so they fit together.
Gerald