I agree the value packed into the nMP is decent, (and compares favourably with BOXX) but... Is it really true you can't even build a comparable system from parts? That would be impressive.
You probably can, but it also partly depends upon what you mean by comparable; do you mean same or similar operating performance only, or do you take into account factors such as such, noise or flexibility?
The new Mac Pro is a form factor entirely unlike any prior workstations, but should still pack similar performance into that small size. It may also potentially be quieter and more energy efficient.
Flexibility however is definitely something that suffers; for example if you're building a 12-core machine then your own option in the Mac Pro will be a single 12-core processor, which is likely to cost a lot more than a dual 6-core machine would cost.
The D300 and D500 GPUs also have some significant differences to the corresponding FirePros, mainly in terms of VRAM but also in a reduction of core clocks. The D700's have the same VRAM as the corresponding W9000's, but do seem to also have a lower clock if the rumours are true, though not by a huge amount (it's still very fast).
You're also paying for two GPUs whether you need them or not; if your workstation requirements are more modest you could definitely build a less expensive workstation from the same components, but with just a CPU and a single GPU for example.
Apple's definitely offering a well-priced package for the components you get, the main problem is that you have a lot less choice in those components. While upgrades may be possible, I'm not sure they're likely (and would need to come from Apple), so any comparable workstation build immediately has better value from the fact that you can upgrade single components rather than replacing the whole machine.
Also, comparing the new Mac Pro to
only a directly comparable workstation is limiting, as you need to compare it to what you actually need. The new Mac Pro for example has only one confirmed internal drive (if it could handle two I would think it would have been mentioned somewhere), which means all extra storage needs to be external, which isn't cheap and comes with caveats of its own.
This all said, I don't believe the new Mac Pro should be compared only to workstations anyway, as it's not really a workstation anymore. I'd call it a professional desktop, basically more like a traditional desktop, but with workstation components; it's clearly not designed to be super flexible and upgradeable, which is something most workstations excel at and are bought for, but it does look to deliver a lot of performance for such a compact desktop. The real question is whether form factor is important to the people who are likely to buy one. Personally I'm thrilled by it, but my only real requirement beyond the machine itself is capacity storage; I don't need super high performance RAID, or super high density storage, just a few terabytes really, which I can handle external though I do begrudge having to a bit. But I don't know that I'm a typical user.
But then, a typical user is likely to be a professional who will easily cover the cost of the Mac Pro over time, whereas my earnings are all over the place which is why it's harder for me to decide if it's worth it or not economically.