Okay, the reason you're confused is because these files are actually themselves generated by a GUI, not by hand. As a result, they're not really intended to be easily edited or understood by humans. The GUI tends to leave behind a lot of unused values (such as Parts in "Cockpit Armor" or Part and Avoid in "Weapons") and sometimes changes the order of things.
The ship generators are also a really old system that I haven't really maintained as the game has evolved. Originally my thinking was most of the ships in the game would be procedurally generated, but for both design and performance reasons I've since decided against that. I've thought about deleting it altogether, but I'm keeping it around because it might come in handy some day.