The skills of "programming in the large" are hard-won through experience. There is no good "theory" that will help you structure a large program (despite many languages from academia making the claim of good structure). That's just one example.

In my experience, it's easier to teach a programmer CS theory than the other way round. At least the programmer knows what he doesn't know.

I think you misunderstand what I mean by "theory" and "theoretical background." Knowing how a computer works from the silicon level up to the operating system helps you design systems, and starting with that foundation helps you build better systems. You can get the same experience after a theoretical education, but you can't fake a theoretical basis from simple experience. You're right that you can learn it, but in my opinion, having the theoretical foundation is key to getting the right type of experience, and also helps you immensely along the way.

All I know is that I look for it when hiring. A Berkeley, Stanford or MIT CS student has a very high weight. They still have to prove themselves, but they definitely have a head start in my book.

I'm not sure I agree. For practical programming, design is one of the most important skills that you need. Code that is ugly is automatically unmaintainable, no matter how theoretically sound. The text editor is your canvas, it is your job to turn out a work of art.

I believe this is why so many without strong CS backgrounds are successful as programmers: They bring the design skills often lacking in CS graduates.