In this RAID setup, App and File would not be on the same Drive. You'd put the App on the C Drive, which is the 20GB Hard Drive, and then you'd get 2 40GB Hard Drives and put those on the RAID array and use them as the audio drive only.
I may be misunderstanding how it works, but AFAIK, RAID drives have to be the same size, so the 20GB system/software drive wouldn't be included in the array.
When you say ProTools doesn't support Dual Monitors, does that mean it doesn't on the PC, either? I mean, can't you drag a window from one screen to another?
Now what about performance? I mean, there are PC users and Mac users out there, and they are happy with their systems, so the question may be moot, as it might just be personal preference.
All the talk is leading me to think a Mac would be the better choice overall, though. I'll just miss that right mouse button.
I know there are Mac 2 button mice, but I've used them and they aren't exactly perfect.