PNPM’s primary feature, even if it gets lost in all the optimization, is make it work, make it right. With an emphasis on the former serving the latter as the goal. FS links are an implementation detail. The thing it gets right is resolving only the dependencies you specify, unless you very clearly say otherwise. The way it does so just also happens to be efficient. If it’s confusing any other tools, they’re doing something wrong too. Links aren’t some wild new concept.