I know nothing about xcode, so I don't know if automating the manual editing is at all possible (to build under Windows, there are also a couple manual steps to follow when building with VS2010 Express, which are not in cmake's control), but as long as you keep the changes between "if (DARWIN) ... endif (DARWIN)" sections in the cmake files, you should be safe from breaking Linux and Windows builds.
You will probably want to make the changes inside indra/cmake/00-Common.cmake, since this file is included by pretty much all other cmake files.
Also, do have a look at LL's v3 viewer cmake files and see is some DARWIN specific stuff could apply to the Cool VL Viewer.