You still need to have those symlinks checked. For example you switch branch to one with updated package.json, now you need either to check symlinks or you risk to have incorrect build.
Introducing a directory that needs to stay in sync with dependency manifest will always lead to such problems. It is good that Python developers do not want to repeat such mistake.
Just run `pnpm install` after switching the branch. Or add `pnpm install` into the build step. And many build tools will do that automatically. If the deps are in sync with the manifest, that takes typically less than a second.
This is a problem I've never encountered in practice. And it's not like you don't have to update the dependencies in Python if they are different per-branch.