Second this. I'd ask that any dependencies in node_modules/ override whatever is cached.
For a work project, I'm updating a dependency written against an undocumented specification. Much fun is being had doing this, I assure you. Being able to crack open the sources in node_modules/, instrument things with logging, and fix fix fix until I get something working is very helpful. I'm sure I can track things down in a cache directory and do the same, but it's nice knowing that my changes are limited to just this particular project, and that a checkout/reinstall of the module in another project will get the original broken sources for comparison.
For a work project, I'm updating a dependency written against an undocumented specification. Much fun is being had doing this, I assure you. Being able to crack open the sources in node_modules/, instrument things with logging, and fix fix fix until I get something working is very helpful. I'm sure I can track things down in a cache directory and do the same, but it's nice knowing that my changes are limited to just this particular project, and that a checkout/reinstall of the module in another project will get the original broken sources for comparison.