sensor – How are focal lengths derived from camera calibration (resectioning) and pixel sensitive area related?

In camera calibration (camera resectioning process, e.g. camera calibration with OpenCV) does the result for focal lengths fx and fy depend on the photo-sensitive area inside the pixel ?

If I have a camera sensor (CCD/CMOS) with a perfect square grid arrangement of pixel elements, but each pixel element has rectangular pixel sensitive area (photodiode).
For example, pixel dimensions are a x a, but photosensitive area dimensions are 0.5*a x a.
Would result of camera calibration still be fx = fy ?

And what if the pixel sensitive area has some arbitrary shape due to additional electronics in CMOS ?