To her credit, Stephan's comparison of PhD earnings compared to BA/BS earnings is better than most I've seen. For instance, she compares BA/BS holders who have been out of school for a few years to PhD holders who are new in the job market, to reflect opportunity cost. Not everyone does that. Also, she limits her analysis to PhDs and breaks them down into three categories, whereas I've seen analyses that lump together ALL doctorates. As much as I'd love to think that my compensation is comparable to that of a dermatologist, the sad fact is that it isn't.
There is one weakness, though, albeit one that is common to all such analyses: The average person with a PhD was probably more talented when they finished college than the average person who majored in the same subject but didn't get a PhD. Note the "on average" part. Of course there are dumb PhDs (just come to a faculty meeting...) and of course there are brilliant people who never went to grad school. And of course there are people who never got a graduate degree but made outstanding use of people skills that aren't a direct part of a research degree (though they can of course contribute to research success) and there are people who got a PhD but can't work with others, and yadda yadda.
But with all of those necessary disclaimers out of the way (to head off a flood of anecdotes that people always feel the need to pour forth when you make a statement comparing two groups "on average"), it's likely that most (not all) of the people who get PhDs were in the upper tier of the talent pool before starting grad school, and they probably could have done quite well in the job market even without a PhD. Her analysis doesn't account for that. To be fair, nobody else does either, probably because it would be really, really hard to account for that. Still, it's a caveat that needs to be applied when looking at those income premiums. You don't know how much is a premium for the PhD itself and how much is a premium on traits that they possessed prior to the PhD and differentiate them from the average person with a BA/BS.