I had no idea about the differences (or apparent rarity) until recently when I started to look into it.
I haven't done an extensive study, but just at a glance there were some pretty significant differences to how the black/brown overlay plastic was held onto the white part. My Chelco used melted plastic tabs to hold it in place, while the other one used several screws. Also, while the Chelco motherboard fits into the other case, it looks like there may be some slight differences with how the corners of the PCB were meant to be held by the two halves of the plastic case. The motherboards are of different revisions and RF shield styles as well, so that also makes a difference with how they fit.
The two sets of plastic definitely came out of different molds. There are a ton of visible machine tool marks on the inside of the non-Chelco. Either they didn't do much finish work on the mold, or perhaps it's an early test run that they deemed good enough to slide for production before the finalized their mold. The Chelco looks considerably cleaner in that regard, plus it also has their name as part of the mold.
I'll try to get some macro pictures... It's not the most exciting piece of Atari investigative work but I still find it interesting that they were using different contract manufacturers simultaneously.