From that doc page it sounds like that
should be deterministic? Even without shrinkwrapping, a fresh install from package.json with empty node_modules should be deterministic.
> The npm install command, when used exclusively to install packages from a package.json, will always produce the same tree. This is because install order from a package.json is always alphabetical. Same install order means that you will get the same tree.
> You can reliably get the same dependency tree by removing your node_modules directory and running npm install whenever you make a change to your package.json.
Maybe you're experiencing a bug, rather than some in-grained non-determinism in npm?