Speaking as a seasoned Node.js dev, if they think they can handle Node's nested vendored packaging system using flat debian packaging and guarantee correct behavior of the app they are sorely mistaken. It's a fools errand. The sheer amount of effort being proposed here is astounding.
It's not the first time debian package policies seem backwards and trying to shove a square peg through a round hole. I hope the solution does not end up being "make APT do it" because APT is a terrible package manager to begin with (I hate every second that I had to fight APT over how to handle PIP packages that I would very much like installed globally).
The problem here is packaging, and maintainer decisions. And yes, I'm familiar with the issues here, and the bugs filed. I think it was handled... improperly as well.