Webpack has the very useful "chunking" system which is able to figure out common dependencies, and based on how often they are re-used across your app, determine whether they should be bundled separately. It's really good if you're trying to find an optimal balance between the number of files on a page and the cacheability of each one. I haven't seen that feature in Browserify or other module bundlers. Of course, with HTTP/2 server push hopefully a lot of these issues will go away.
That sounds like exactly the sort of magic they are talking about. I'll take predictable over magic any day, in this case it sounds like the sort of decision that's best left to people anyway.
