I still think removing "--enable-node-worker" shouldn't make a difference, if you don't use C3 worker mode to begin with. There is probably a different underlying cause for NWjs to not close properly. I'd recommend checking out the browser console after long gameplay sessions, maybe there is a script error or similar that's preventing NWjs from closing.
As a side note. I'd recommend doing OS specific steps on the OS itself (even if it's done in a VM). Unzipping MacOSX game files on Windows could mess up OS specific permissions, causing issues later. At least that's what people exporting games for those platforms told me.
NWjs can be a pain sometimes but it's alright if you just write down and do things step by step.