Here's what I inferred from https://thebookyard.wordpress.com/2014/04/09/apple-part-numbers-explained/ :
The APN part number is the part number that refers to a certain version and model of a component. Apparently, this can change based on minor revisions, manufacturer changes (sometimes Apple uses multiple manufacturers), and other things. You could compare this to a lot number of a medicine. Each time a drug manufacturer makes a small change to the medicine, whether it is color or packaging, for example, a new lot number is assigned. In the event of a recall, they can use the lot number to identify the specific batch that is affected.
The part number that appears in GSX is a part number that refers to the actual part. This normally stays the same through minor revisions. To continue with the medicine analogy, this could be like the UPC barcode on the bottle. The medicine is still the same (for instance, if Tylenol decided to make a change to their cherry flavor), but slightly different ingredients.