This is more or less what I was taught, although not necessarily due to protamine (you would use the rapid before Lantus, too). I believe it's mainly the fact that you're putting something with a longer duration into a vial that's supposed to be short acting, so you could get a peak at the wrong time and end up bottoming out.
Also with the cloudy NPH, if you get some of that into your rapid, it would probably make the whole vial cloudy, so that's obviously not desirable.