It is funny - half of the real desire/need for containers comes back to these sorts of issue with both node and Python. And then they bring in their own different challenges.
Node's dependency managers npm/yarn just copy the versioned dependencies from their cache folder into the local node_modules folder and remove transitive dependencies duplicates when possible by flattening them into node_modules.
So I spent 2 hours and rewrote it in Java 8 with Maven.
Issues all gone. Node has some work to do before I’ll consider touching it again.