You do gain skills with a humanities PhD, that was the point of the pro-PhD piece. The development of serious research skills, critical thinking, and writing is something applicable to a wide number of jobs out there.
The skills you describe can be gained by job experience, and this is much of what chemistry grad school has become: a substitute for on-the-job training. You can see that there are very few jobs for zero years experience out there because industry is using graduate school as a way to get out of investing in its employees in the form of training. (and please note I'm not saying that graduate schools are not complicit in taking advantage of students in the current system to meet their own ends)
Call me old fashioned, but I don't think a PhD should equal simply five years of bench experience. It's about the problem solving, writing, and critical thinking skills - the deeper understanding of a subject AND how to develop deep understandings of other subjects.
Right now someone may go to grad school for organic synthesis and then think they've prepared for a job doing organic chemistry. I think if someone gets a PhD doing organic chemistry, they should be prepared to do a broad range of chemistry (or even some non-chemistry) jobs because their value isn't in their knowledge of organic reactions, but in solving complex problems and teaching herself or himself (learning) the new skills they need to address those problems.To his comment that you gain skills in a humanities Ph.D., my question is, "At what cost?"
I believe that the main reason that there are relatively few entry-level positions in chemistry right now is that corporations don't see sources of future economic growth in the West. You hire newbie PhDs for research; if you foresee flattish economic growth in the developed world right now and no obvious sources of expansion*, why invest in new workers that will cost you money now and might pay off in the future? It's not a coincidence that pharma was hiring like crazy in the late-90s when the sky was the limit on pharma's stock price and the US (and the world, it seemed) was in the midst of limitless economic growth.
I agree with Andre that a Ph.D. in chemistry should have signaling value to other fields and show that the holder is capable of complex problem solving. I think my problem is this -- other fields have certificates and signals of their own. Even if we all know (and we do, don't we?) that chemists are master ninjas of problem solving, I have yet to see other fields poaching Ph.D. chemists and allowing substitutions of the Ph.D. credential in lieu of their own special credential. (Sure, there's the odd hedge fund and think tank.)
Even within chemistry itself, it seems that we only hire from our unique subfield. While I'm more than prepared to believe this is
*That should be "no obvious sources of expansion that do not have their own built-in sources of research scientists, i.e. India or China."