First is the model/API for actually writing your app. Web Audio is very imperative and, in my experience, doesn't handle dynamic behavior terribly well. Elementary is designed both for functional/declarative expression and for change over time.
The second piece is that Elementary is built around a core runtime which can be embedded anywhere. Web Audio is, as its name might suggest, quite coupled to the browser environment. My goal is that if you've written an audio app that runs at the command line with Elementary, you could package that same thing up and ship it as a VST plugin, on embedded linux hardware, etc.
I was wondering how you feel about the idea of taking advantage of the fact that your frontend can run in any browser, in maybe considering a "remote gui in the browser of your choice on any LAN client" kind of thing.
The processor itself could be headless (not sure how Elementary is implemented, I see you mention node.js, just having an immediate reaction, maybe it already is gui-host-agnostic network-aware in that sense, by default, open a port to the lan, etc)