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Why does Fink install libraries that are already available on Mac OS X? Is it because the libraries are outdated or certain features aren't enabled on OS X?
Many of Apple's libraries are indeed older than the newest upstream. (openssl is a good example). Others don't have all the necessary features. Apple's python for example doesn't have any X11 support (and is also only python2.5 vs 2.6 as the newest).
If there's a package that uses Fink's libfoo but you want it to use Apple's libfoo (like for example minimize the dependency tree), your best bet is to contact the package maintainer (fink info <package>) and ask them if it's possible to use the system library. Sometimes it will work, other times it just won't be possible.