I worked in a lab that used all the techniques listed and then some.... As with any sort of failure analysis there is the potential of destroying the part. However, it's not as difficult as the article makes it sound. Within a square mile of where I currently work there's at least 4 labs, including the one I'm in now, that have and use all the equipment listed in this article.
I also can't fully agree that it would require little investment on Apple's part. This may be the case. However, it seems to assume that Apple has built in a back door, which it may or may not have. I've worked for PLD companies and dealt with the government, gas (think gas pumps), and gaming industries. We didn't necessarily have a simple way to hack the chips we built. I get the impression that they're saying it would be less expensive for the government to force Apple to do this at Apple's expense than to have to pay a lab that specializes in this type of work.