I have thought about this before (project based, sandboxed).
I work on projects on a different drive to LabVIEW which isn't a problem when working on individual toolkits; as they are self contained. But it got much harder once I started needing the Encryption Compendium in everything I always needed to have it installed in the LabVIEW vi.lib directory and any time I updated it had to reinstall for the other toolkits to amke sure they still worked as expected. So I played around with symlinks placed in the vi.lib directory which worked pretty well and could keep the menus in the IDE. Just replacing the symlink to different versions was also OK and worked but I couldn't figure out a way to stop some VIs recompiling (so just lived with it).
Thinking off-the-cuff. We could probably have an IDE helper to select different VI.lib toolkit versions on-the-fly.