The real comparison comes in how good the machine is at doing what you need it to do. If you're making a movie or doing serious sound editing, video editing, or modeling, this machine and the accompanying software is clearly top-tier, compared to trying to assemble a full workflow yourself that includes the hardware, software, and infrastructure integration. And the fact that you just order it off the shelf and it comes with everything and integrates with everything isn't really priced into this comparison.
This is exactly what people seem to not understand. Not to mention trying to get support when your custom built system starts to have issues (blue screening due to drivers, hardware incompatibilities, etc.. ). When you have a project due for a client and some key piece of software starts crashing, or crashing the machine, the last thing you want to have to deal with are the numerous vendors playing the blame game.
Granted, not all software will be fully tweaked off the bat with the new mac pro, but its a system that no doubt the big players (The Foundry, Autodesk, Maxon, Avid, Adobe, etc) will target for testing and make sure their software works and takes advantage of as much of the hardware as is possible. As opposed to testing on randomly built DIY solutions.
For the price, how can you really beat a high end system thats custom built (down to the pcb level), using mostly off the shelf stuff (just assembled in a way thats not convenient to the DIY/tinkerer), supported by a single company, and is / will be used in testing by the actual companies that write the software you want to run on it?