That way users can get all the package-manager goodness for stuff they compiled locally. And also because Gobolinux lets people install more than one version of the same package.

You've fundamentally misunderstood how GoboLinux works. The whole point of these kind of distros is to avoid mixing packages into a single common directory. Each version of each software are installed in separate directories in /Programs so that they won't cause conflicts with each other. Then for convenience, a single version of each software will be symlinked into /System/Index.

This is way more meaningful than the /bin & /usr/bin split that distros are increasingly moving away from because multiple versions of the same software or forks can coexist on the same system. This model also makes /usr/local unnecessary.