WARNING: TOTALLY BIASED RESPONSE TO FOLLOW.
You probably can get something with similar specs built for cheaper, but can you guarantee that a non-audio industry cumputer shop will give you a compatible system? Can they give a two-year, "bumper to bumper" warranty, plus additional warranties through the component manufacturers? Can you call them when Pro Tools (or Cubase, Sonar, Samplitude, or whatever) isn't working properly? Will they help you configure it for audio, add a restore image, include test files, diagnostic tools, and free training videos? Can you call them any time for support?
The point of getting a custom audio PC is that it is built and supported by people who know and work with computer audio every day. It's ultimately up to you whether those additional services and warranties are worth the potential extra cost.
Lead PC Install/Repair Tech
Sweetwater Service Dep't