One of the places this helps you is when you push out a one line javascript bug fix without invalidating your CSS caching across the entire site, because the CSS files are identical.
It also helps you with people with the website open when the new code gets pushed. They either have all the old code or all the new code and no bizarre mishmash of the two.
It's a bit of a optimization as to be 100% sure users always get the latest files the version naming scheme is needed, but most of the time it will work anyway, eg. if you have no caching layers /CDN etc in-front of the web server. So if you want to shave off milliseconds on first load, go with the bundle, but if you want to save user's bandwidth and make your site/app more lightweight - don't bundle!