It's interesting to hear him say that npm and node_modules are regrets since lots of complaints about Go packaging from people new to Go ask for something similar...
Yeah I was surprised about node_modules as well. I think that's actually a killer feature (that we don't need $NODE_PATH or virtualenv or similar)!
I've found it has certainly helped with debugging. I find it nice that all of my project's code is in one directory.
To save on disk space, use pnpm, best of both worlds!