It is probably true with on-line prices (though at present there is a 10% off offer), but Dell are very open to negotiation even for one-off machines. It seems to depend on where in their quarter they are and whether or not salesmen are trying to reach quotas!
I didn't want to get into this level of detail. What I do recall, is getting a lower price quote over the phone on small order quantities (1 - 5) even on a model that just released (it's been awhile though; Xeon 54xx parts in a DP config when it came out).
Yes all of us multi-tallented folks who can read, add, and subtract.
BTW, comparing two over-priced systems doesn't really count as evidence that the cheapest of the two does not qualify as over-priced!
Unfortunately, it's Xeon, which is overpriced, no matter what you get. Vendor produced or even DIY, as the parts/systems are sold off in smaller quanities, and the markup is higher.
So it's relative only to a small portion of the market.

Those that have retained their senses, will realize they're not that different than the performance desktop parts (no ECC, which is rarely needed), and know they're paying more for crap they'll never benefit from anyway.
All sealed-in-box computers are overpriced. Building one yourself is the cheapest and best way IMO, then you're not paying for the brand and that someone has done the one hour job of putting everything inside
It depends. On the desktop side, usually. Not so much on the enterprise gear though (Xeons, particularly the DP systems). It comes out about the same, but the user spends a lot of time to research and finally build. Not that it's not worth doing, but it will depend on the specific needs. RAID for example, might make a DIY route more attractive, and less expensive (i.e. use a full tower case that can hold the entire set, which is cheaper than external drive enclosures needed with a mid tower used in a ready-made system).
Here's a question. How much of a retail mark-up are we seeing on Xeon parts? I imagine all the manufacturers get them in huge lots far cheaper and mark them up a bit, but it seems like some of the more expensive Xeons might cost more to buy separately and install yourself if you were building your own rig - you'll have to buy the chipset as well. I could be wrong about this, but I take it that a Xeon board is more expensive than your run-of-the-mill i7 board?
Quick calculation using the W3520 sold as a single in retail channels, gives a 30% markup ($370/$284 = 1.30). But system vendors do buy in quantity (where the $284 came from).
Nehalem DP boards aren't as horrible as I'd expected, and are actually less expensive than the 54xx part (LGA771 boards that had the ability to run FSB1600 = 5400 chipset). More on parity with the FSB1333MHz boards (5000 chipsets) in terms of cost at release IIRC.
So if you build with the lower cost processors, and have anything that can be recycled in a build, it might be worth it. But currently, you won't be able to OC them with the boards, as they don't allow access to such settings. Perhaps via a software method, as no enthusiast DP boards have surfaced (i.e. SkullTrail II or equivalent from any other board maker).
