I had similar change regarding crop and position in my system after updating.
In the last Companion version the crop and position setup of camera is taken away.
It is now easy to do Your own setup in camera setup: http://192.168.2.2:2770/camera
Add Parameter Region Of Interest (ROI):
–roi Set sensor region of interest
Allows the specification of the area of the sensor to be used as the source for the preview and capture. This is defined as x,y for the top-left corner, and a width and height, with all values in normalised coordinates (0.0 - 1.0). So, to set a ROI at halfway across and down the sensor, and a width and height of a quarter of the sensor, use:
Settings for my Pi camera: --roi 0.02,0.0,0.9,0.94