Apart from the hassle that OSes put in the way of PWAs (intentionally, but that's another topic), a local Node app simply has a different kind of system access compared to a web app.
Most apps won't need these capabilities to function, but they are there, for all purposes good and bad:
- background activities with fewer restrictions
- less restricted file system and sensor access etc
- ...
sure, many app use this for nefarious things.
But real use cases don't need to be sophisticated rendering algorithms or what not.
I think good streaming apps also use these capabilities, for example, for performance.