If the API for the package is consistent with the gnu version, by Gentoo for Mac OS X policy, we put the package in package.provided with a comparable version number/string.
We do not yet have policy for packages that are provided by Apple and that have a different API than that of the gnu version. I'm opening up the floor here for discussion on this.
What comes immediately to mind is making the said packages a virtual, and then satisfying the virtual in our profile. This should work most of the time, as most packages that use, for example, zip, do not use any of the arguments that differ between the gnu and BSD versions.
-- Hasan Khalil Ebuild/Porting Co-Lead Gentoo for Mac OS X
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