I usually don’t copy the node_modules folder for the reasons you lay out; I just delete it or don’t copy it, and then run yarn or npm install in the new location. Is there a particular reason you’re copying node_modules so frequently?
Just in wanting to keep everything ready to go when we want to make changes to a site. Probably best to delete it as you say and reinstall when needed.
But also on the pnpm front, looking for a way we can be ready to go and still use node_modules. Just not all the copies!