Just to follow up, this version of nwjs seems to do something slightly different with the windows. If I call Graphics._switchFullScreen() or Graphics._requestFullScreen() in a plugin, when I start the game, it briefly flashes into full screen, then goes back to window. If I call those functions through a script call before the title screen (luckily I have pre-title events), the calls work just fine and the game starts in fullscreen seamlessly. (And F4 works fine either way.)
My guess is that the old nwjs used to set the window dimensions first and then process plugins, while this one loads the plugins before it sets the window, so the later call is resetting the plugin calls. But, just a guess.
In any case, if you were using those calls in a plugin to start in fullscreen, you might have to use them as a script call in-game (e.g. pre-title event)... or, this could be something with my set up only. I didn't actually test a blank project. YMMV.