I'm not sure how this could happen as one shouldn't be depending on the directory structure in the node_modules/ folder anyway. Do you have an example of where this might cause issues?
I don't actually know that there's any problem that `rm node_modules; npm install` won't solve, since that would make things the same as a fresh install.
All of the scenarios I could come up with were about long-running installs, rather than new deploys, so more likely to happen on dev than prod.
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?
I don't actually know that there's any problem that `rm node_modules; npm install` won't solve, since that would make things the same as a fresh install.
All of the scenarios I could come up with were about long-running installs, rather than new deploys, so more likely to happen on dev than prod.
ETA: actually wrong, see below.