I was actually just thinking about this the other day..
Regarding the flat twin and aero, I think the concept lends itself quite well to undertray packaging. Presumably the engine can be tucked further forward than a similar V or parallel engine, which should allow for some aggressive early rising tunnels. The longitudinal or vertical crank would probably be a necessity for this.
A V twin with a longitudinal crank would also suit this concept very well (in fact probably better), but it sits farther back and doesn't provide as much space in the rear of the car. Space for something like a gnarly Maryland style wing, and more expansion area for the undertray. I don't have a lot of experience working with aero though, and agree with Rob that it's all just heresay until someone goes and does it/models it.
On a similar, more fantastical note, if someone were clever enough they could take the exhaust from each flat cylinder and use it to boost the undertray. That would raise a whole host of other potential issues, but hey it's worth thinking about.
Edit: John beat me to mentioning the exhaust blown aero, damn. As far as I know, it is completely legal.