I thought about that, but clearly they have enough information to figure out whether to load the package from the top level or a nested directory. (I'm guessing simply by bubbling up and looking for the "node_packages" directory.)
It doesn't seem too big of a leap to do it the way I was suggesting.
Either bubble up and look for "node_packages", but this time store a symlink there, or add a dot file that tells you "this is where I found package.json".
I'm sure there was a reason they didn't go for either of those solutions because I've followed the team's discussions when they were iojs, and they have very smart people. I was just curious about the reasoning :)