The former seems to be more polished, while the latter seems to be more complete.
Do they differ in any other way, and am I missing the "full version" out there, somewhere?
The one on TLG's site is probably the preferable one.
That version I piled in every OGC source I could find. I also used d20 sources to fill in some gaps. Some of the conversions I did could probably use some better treatment. I had never played or ran a game of C&C nor 3E (Still haven't played 3E
The second version, I condensed a lot of things. Example: Instead of a bunch of races, I wrote up some tables on how to use monsters as races. I also started removing material that was already covered in official books. The problem with this version is that I started adding in random generic stuff (like Adventure Seeds) for whatever reason and there is some unfinished conversions in it. Also, the pdf export seems to have lost some pages.
This is the current version https://www.dropbox.com/s/l0i4ldemedchy ... n.pdf?dl=1
I started with a blank slate and slowly added old material to it, while being more careful with converting and consistent formatting. It is incomplete and I'm not sure when/if it will ever be. C&C isn't really my thing anymore, I moved back to BECMI.
I could be mistaken; But the Black Tome of Narutus from The Haunted Highlands material has the Necromancer within its pages I believe. The information within the Companion may be building from that.
This is the correct answer.