There's a world of difference between a general-purpose computer and a specialized device like the Rift. The computer has its own independent utility and stands on its own merit, the Rift is an entirely optional upgrade that nobody has to purchase. To make a car analogy, most people are going to buy a car to get to work. But you should still evaluate all the optional extras on their own merits, unless you're just too rich to care. The proper way to evaluate a lift kit is not "well it's twice what it was advertised as, but that's still only 25% over the base cost of the vehicle".
Regarding the other things - the fact that nice components exist is entirely irrelevant to the failures of expectation management here. If NVIDIA spent 2 years marketing the Titan X as the best GPU to have at the $1k price point, and then on launch day it's suddenly $2k - their customers would very justifiably be pissed and it would certainly affect sales.
It's neither here nor there, but you can also cut build costs quite a bit further than they did in that article. You can bring it down to about $800 for the same set of core components. Buy the CPU at MicroCenter, use the stock CPU fan instead of a cooler, buy a refurb 970 from EVGA, look for a 750W Gold PSU around the $50 mark, buy a cheaper mobo, buy cheaper memory. You can even go cheaper if you make some minor compromises - use a 2500k and overclock, get a refurb 780 Ti from EVGA B-stock (same performance as a 970), and you can also drop the HDD until you really need more space. That lets you squeeze at least another $200 out of it pretty easily without affecting performance, which would get you down to around $600.
