Here's a short list of factors that could contribute to the results the article in OP has:
-Lower number of years working in the field due to taking time off for maternity leave, or going back to work after raising a child. I suspect this is probably the biggest single contributor to the pseudo-gap in the article's charts.
-Concentration of male/female developers in different subfields. Ex: men may be more inclined to work in security penetration, which may pay higher than other disciplines
-Male/female college degree/other pedigree rates
I'm no statistician, but I think these factors are more than important enough would have to be taken into account when trying to figure out the size of the gender wage gap.
Don't forget to leave a comment telling me why I'm wrong when you downvote my comment for being unproductive.