I've just found that selecting an OSX Base SDK, OSX Compatibility Version and OSX Architecture don't seem to have any impact on the generated project in Xcode 5. Regardless of what I select, the project is set to No SDK (Latest OS X), Standard Architectures (64 bit) and 10.9 for my Deployment Target, for both Debug and Release builds.
I've just upgraded to JUCE 3.0 and the newest Introjucer, but I've never used these features before so I can't comment on whether this is a new thing.