The more I look into it, the more I like the stacked approach - sure, you could spin a single board for almost any application, but, this will allow you to easily make any fully isolated board, really handles the modular approach (I would probably have a peak-and-hold card as something in my first build - I'm not driving/testing without it, it interests me on it's own, and I see it as being crucial to the widespread acceptance of the project). I like the idea of making cards without it being a total hack - the more MS "develops" the more of a joke it appears to me. The code is as hacked and tacked together as the hardware, and I'm embarased to see a board which sits in place of a board which is meant to simulate some old chip that no one would ever use and jumper cables here and there.... Make a P&H board on the bus and you know everything is good. And if you really have a power board and a non-power board, I think you could have one power supply for all the "controls" stuff, and only resort to a second/clean supply for the big things.
I already own Jean's board, and I'm not that hot to use it. I would if I had to, but ... I'd want to at minimum do more digging into some of the existing hardware solutions. More and more smart IC's are out there for automotive applications.
Then again, I'm building 7 card stacks for a living.

Oh yeah - the windows and linux versions keep stuff in different places. It's pretty gosh darned annoying.