Per John Z, cars built with rear quarter louver trim had mounting holes pierced in the quarter panel. This was done with a fixture placed on the quarter panel at a station somewhere during body fabrication. Writing the code was probably something a manufacturing engineer cooked up to ensure it was completed as needed; no one wants re-work. The X codes may have referred to pages in an assembly manual. I have never heard of a Van Nuys car with an X code written on it.
The late Warren Malkin had an X44 COPO; the passenger side of the car had the louver holes punched and puttied shut prior to paint.
Could be it was only done for red, green and blue interiors.