If you're a software engineer with the skills to mess with low level interfaces like that, $200 doesn't seem that insane, especially since those are general purpose boards that can easily be repurposed. I mean of course I realize that for many people $200 is a lot of money but I'm willing to bet that for the average HNer it's really not that big of a deal.
Besides TFA's chip requires desoldering and resoldering an SMT chip from the RPi's tiny and densely populated motherboard, not exactly Soldering 101.
Moreover if you're really just starting with low level programming, want to mess with basic electronics and things like that then don't get into PCIe, actually don't even get into Linux. Just get a cheap-o ARM microcontroller board, a multimeter and a $10 saleae digital analyzer clone from ebay and play with that, you'll learn a lot more that way.
$200 isn't a big deal for something you really want, but at the margin, on projects that you don't even know you're going to bother finishing, it's the difference between being able to justify taking a punt on it and not.
That's why the Raspberry Pi is so popular.
I agree with everything you said about using cheap microcontrollers to experiment with basic electronics projects.
