Let me begin by addressing the idea behind the "Building Your System" article. The article was written as a personal "wish list," if you will, of products that Roger Maycock, Randy Alberts and I would consider purchasing. The idea was to give the reader some ideas and to get you thinking. That said, I'm a Mac guy through and through, and thus I based my DAW purchases accordingly.
You do, however, bring up some very interesting concerns regarding Pro Tools LE for Windows and cross-platform compatibility. I contacted Digidesign, and they concede that P-T LE 5.0.1 does not support MacOpener, which is required to mount Mac-based HFS and HFS+ drives on a PC and share files accordingly. This is something that Digi plans to have cleared up with the 5.1 release. As far as sharing files between Windows-based TDM and LE systems, Digi insists that the two systems are compatible if, and only if, a FAT 16 drive is used. I hope this helps and good luck.