Dumb question: when considering a company that sells branded generic laptops, why not buy from the generic laptop vendor directly (Clevo in the case [0])?
It supports a company selling linux laptops, and they make sure everything works out of the box, and provide support. Pretty much the same reason to use their OS, which is basically just Ubuntu + drivers. It should all "just work" which is exactly what a lot of people expect from a laptop.
If you have a desktop system that's giving you problems in linux because of incomparable hardware or crappy drivers it's a pretty easy to find what component is working well for other people and swap some parts, but laptops are such a pain I don't even want to open one up if I can help it. It sounds like System 76 works with Clevo to put together certain builds they might not offer normally. Why risk getting a similarly spec'd Clevo only to find out it's got a different wireless chipset or GPU variant and now you're stuck with a bunch of of problems to try to work around.
I bought my S76 laptop via my work's "choose your own workstation" program. It's a great way to support continued development of the software I use PLUS when you buy via S76 you get lifetime support for the device. The support is not something I've made use of often, but it certainly paid off the one time I needed it. Basically, it depends on your idea of "value" - do you value money (buy cheaper hardware) or time (buy S76 with support)?
Yea, I had to pay for the battery, but when my battery died they shipped one out immediately with free shipping for the cost of the battery (no markup from the "aliexpress special" I found later; and I bet theirs is more reliable than that one). Also, when I had password issues with FDE due to my own failure, after the warranty ran out, they emailed back and forth for days until we fixed the issue.
I bought a NUC from them years ago that was always a bit wonky, but not unusable. Until one day I couldn't stand it any more and sent it back for repair. At that point I'd had it for well over a year, maybe more than two. It came back with a fixed controller and has worked flawlessly ever since. So, you pay for support. And the price difference is peanuts compared to all of our hourly rates.
No, they co-design the laptops and ship them with completely different firmware. That's very different from what you're saying is happening. You even linked to a thread where an employee discussed how it works.
It'd be nice if they made the laptops themselves, but not even Apple does that.
[0] https://news.ycombinator.com/item?id=17039414
(Yes there's a response in that link from S76 folks but I'm still curious on the buyer side your reasoning.)