Chipmunk should just build out of the Box. It uses no special APIs other than the C std library. The only gotcha is that you have to compile it as C99 code, but this shouldn't be an issue unless you are trying to use something other than GCC to compile it. The only thing that the "unofficial" port did as I understand it was to change the Demo code so that it it would work with OpenGL ES/Cocoa instead of normal GL/GLUT.
As far as a Chipmunk/Box2D comparison: Box2D is much more feature complete, hands down. (Especially with the new version that was just released) I originally started with the Box2D code and added a bunch of features (collision groups and layers, more collision types, collision callbacks, better broadphase collision) most of that has been implemented in some way or another in Box2D now as well and then some. One potential is that it has a C++ API that isn't going to play all that nice with Obj-C. (though if you are going to code the majority of your game in C++ anyway...) I would guess that Chipmunk is faster, but I don't really know. I've gotten a lot of compliments about Chipmunk's API being easier to work with than Box2D's, but YMMV.
On a side note: I actually saw the Chipmunk demos running on a coworker's iPhone. I was pretty surprised at how fast the little things are. I'm pretty pumped to try my hand at some iPod Touch physics programming in the near future.