The actual signal level on modern mastered CD's can be literally -.01 dB short of full scale, but the resolution of the mastering meter circuit under real-time conditions may not discern between this level and 0dBFS (max/clip). It is quite common for manufacturers to implement a circuit that illuminates the CLIP indication PRIOR to actual clipping, so that the engineer can correct any issues before an audible result is heard.
It's also been my experience that most professional digital recording equipment also use limiters to prevent clipping in any case. Extreme amounts of compression also make it easier to prevent clipping, at the expense of dynamic range.
If the source material was indeed clipping, it would be quite noticeable. This type of clipping is particularly annoying and very hard to cover up.
But since this is a theoretical measurement with test tones and not actual source recordings, I'm not sure what the point of the article is. Is the author suggesting that there are CDs out there that clip? I would think that they would be pretty rare and pretty amatuerish as most good engineers are quite aware of what happens when the signal actually clips.
Don't get me wrong, I've heard plenty of CDs that sound like crap, but I've never heard one clip unless it was intentional or mastered by a complete novice or moron.
Has anyone heard a CD that this clipping was noticeable? I'd be interested to giving it a listen.