Yeah - the npm client codebase would not be fun to do a big refactor on. And you would need to do a big refactor to make the v3 flat install process deterministic and/or performant.

These issues have been raised a few times, along with the shrinkwrap/reproducability stuff, and it didnt seem like it was a big priority for the core team. Understandably I guess they seem more focussed on the enterprise/private repo side of things and just keeping things running on the client side.