I think one of the points you missed in the article is, the sorts of systems the article was talking about, for want of a better term, evolve themselves.  So the programmer may know what it's doing and why initially, but after a few thousand, or million, training runs, he won't be able to say "this is the portion of the code that made it do X" anymore.  This isn't an "open source vs closed source" sort of thing, it's more a "I built a tool and now the tool has learned how to do things I didn't originally build it to do."

You built a piano playing robot that can be "told" by passerby whether they like what it's playing or not from a built-in library of tunes, and now it's creating it's own piano concertos from whole cloth.