What exactly is the problem with some large files? Sure, I guess it's quite a large number, but what really is the concern? If you're worried about download size, then you'd be crazy not to compress it, in which case the total numbers are 46mb for win32 and 55mb for win64 for moderate compression (just Windows' add-to-zip feature, so you could probably get it lower with better compression), still not a lot compared to the average desktop game download and not long to download on broadband. For the uncompressed size of ~130mb, are you worried about the disk space it uses up? This is a drop in the bucket for most modern desktop systems, which easily have hundreds of gigabytes of permanent storage. Maybe you think it affects performance? It's large because it's bundling the entire Chromium browser engine, which has generally had the best performance of any browser - file size does not itself affect that. For example modern operating systems are efficiently designed enough to not even read from disk parts of a DLL/executable file that are not executed, and CPU caches are only concerned with the data that is actively in use. So it's perfectly possible that a very large file still be highly efficient. (Consider also most operating systems themselves are very efficient these days, but have colossal install footprints in the gigabytes.)
If you are anticipating a 200-300mb project (presumably the compressed figure, since usually most of that is already-compressed PNG, Ogg Vorbis, etc) then an extra 55mb is only a moderate overhead relative to the size of the game itself. If you had a small project then it can be a high overhead relative to the size of the game, but then you can work around it another way: everyone in the world already has a browser installed on their computer, and you can publish as a HTML5 game to the web, with no overhead at all.
We've been using node-webkit/NW.js for a long time now, and very few people have complained about the filesize. I don't think it really materially affects anything.