I've been spending a lot of time in the embedded area lately (sub-200Mhz 32k RAM automotive systems, firmware and fpgas) and I agree with you. But there's always tradeoffs. In this case you're trading some memory (which is cheap nowadays) for up-to-date, secure, usable apps, which seems to be a pretty complex thing to do. Nobody solved it so far. The people using node-webkit are offloading the library compatibility issues to the people who built Chromium and are provided with a consistent container to run their application in.

The software that we build tends to gain layers. In theory, each layer adds new functionality that couldn't be done on a lower layer. The problem comes when someone unnecessarily implements lower functionality in an upper layer (like reading local files through a web server). It happens because systems are too complex now for a specific dev to know every layer, and new hardware is fast enough that it doesn't matter that you're taking an order of magnitude more resources than you actually need to do the task.