One thing this article leaves out is the sky high attrition rates in PhD programs. The grim statistics presented are for the people who actually finish. Overall attrition rates for PhDs in engineering, the best of the bunch, are about 35%. It only gets worse for science and humanities. Keep in mind that attrition rates for elite law or medical schools are generally less than one half of one percent. So it is no exaggeration to say people fail out of elite PhD programs at roughly 100 times the rate for elite professional schools.
It does frustrate me to watch congress base public policy on the notion of a shortage of scientists and engineers when the evidence clearly does not support that assertion.
I'm not sure that all of them fail out. When I got my masters, the prevailing wisdom seemed to be that you had a better chance of being accepted if you applied for a Ph.D. and then quit with a Masters, which is what I did. Also, many of the other posters here decided that the job prospects were terrible and quit.
You are right that "mastering out" is not the same thing as failing out, so I may be overcounting here. Universities do also use the trick of admitting aspiring PhD students as MS students first, so that it doesn't affect their numbers when they fail to enter the doctoral program later. So there is also a possibility of undercounting as well.
I need to think a little more about this, but you're certainly correct in pointing out that it is more complicated that what I wrote - especially in engineering or CS, where an MS makes sense as a terminal degree goal.
It does frustrate me to watch congress base public policy on the notion of a shortage of scientists and engineers when the evidence clearly does not support that assertion.