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.