I think it's more accurate to compare Node to C++, compare NPM to apt/yum/etc+CMake, and compare something like Electron to Qt.

Of course, your point still stands. But's a tradeoff. C++/Qt has a ton of compile-time bloat, while Node/Electron has runtime bloat (see the Slack client using hundreds of megs of ram). And you can use bindings, like PyQt, where you have Python/Qt and then you get Python's dependency management.