You'd have to ask Puget -- and I think you should.
And I have...
RoGuE, there is time and value.
As the owner of Puget said in the thread for the first version
First, on pricing -- we definitely don't compete with building it yourself, and we don't try to. If you have the knowledge to pick the right components, the ability to put it together, the tools to test for thermals, balance the fans, ensure you're running at safe temps, and the patience to deal with any issues that may come up (including RMA'ing parts), then you can certainly save some money by doing that. We're here for the niche audience that understands the importance of quality hardware and craftsmanship, but who do not have the time or ability to build a PC themselves. And I think that audience is growing when it comes to quiet PCs. I've seen far too many people try to build their own, who end up inadequately cooling their PC.
Their effort is worth something, and cherry picking parts is worth even more to me.
That said, since I've built more systems than I've bought, I do have a bit of sticker shock over this one. Not only is there a base profit built in, but every part upgrade costs a premium as well.
Like DaveLessnau did in the other thread, I've made a public wishlist
on NewEgg to approximate the system. To paraphrase him: Without the "Quiet Case Fans Upgrade Kit," "AcoustiPack Acoustic Composite Sheets," and warranty/labor/odds and ends, I come up with a roll-your-own equivalent price of $1,805.88 (or $1,978.34 after tax and shipping).
In the case of the system I want, I have to decide if what they are providing is worth $1000.00 to me.