I can't think of any scenario when one would be relying on a specific structure being in the node_modules/ directory. And if there is such a need, then it's likely the code is doing something very strange or very special in which case this kind of package would not even be considered during creation (and I still think wouldn't cause problems).

Even in long-running installs I still don't see a potential issue here. Do you have a small specific example you can think of?