What I've found is that if you install Boost via Brew or MacPorts you're likely going to have issues.
Apple's new compiler and linking tools is having fits with code compiled by the GCC system from what I can tell.
I've started rebuilding Boost from source and have been able to eliminate "boost::filesystem" link errors.
Still wrestling with the program_options library for some reason.
Building your own libraries is definitely a key step in setting up a compiler environment for both OS X and Windows (especially Boost). As far as the undefined symbols for x86_64 errors go, are you sure that the file you're checking is the one that's actually being linked?
Totally agree here -- just wait until you get to packaging up a wallet for release ;-)
Oh the fun you'll have fixing and patching up the dylibs you will need to bundle with it
-dvd