I've been working on this and it does need to be thoroughly fixed.  There are two different aspects to it: (1) being able to build Python using any of the supported development environment options; and (2) support in Distutils and packaging to build extension modules for any of the supported development options.  With the release of the Command Line Tools for 10.7 and beyond (and with the dangling mess of 10.6 with both Xcode 3.2.6 and Xcode 4.2 installations out there), we need to be able to support multiple options for users and builders of universal builds.  Apple does supply tools to deal with development environments installed in arbitrary locations (primarily, xcode-select and xcrun) but there are some gaps in them for supporting command-line-based builds, like a convenient way to find the absolute path to the SDK.  I'm working on patches for all of this right now.  I'm hopeful we will end up with a major increase in usability to users of universal builds.