I haven't driven the S2000, but from what I've read, the 987S is more similar to the later model S2000, which are less apt to bite the driver for mistakes in weight transfer. The point being that the early S2000 models didn't communicate problems well enough. In comparison the 987S is often held up as a car that is easy to push hard. There is probably some truth to your comparison.
Comparing M3 vs. Boxster is tough because they are very different cars. I guess if you try to isolate steering feel, I agree with your comment. So many other factors make that a tough thing to isolate. To me, M3 is all about the engine, with the suspension and handling intended to manage the power. The Boxster is a car that frankly "overhandles" compared to the power it makes. It could easily stand up to 350-375 HP without getting tough to manage. In general, the mid-engined Boxster seems to have much better balance. Making these general comments just to explain that I do not find the M3 an easy comparison...