You know what, I could give it a try. I still am unconvinced by npm's decision to flatten the dependency tree, so I guess anothr approach is welcome.
Do you plan to support yarn.lock files as well?
I still think === is the way to go in most of the cases. Object.is has an advantage when dealing with some numeric edge cases, but that's pretty much all. For the est, it's more verbose and less readable.