Standard caution here:  Saying "Men are different from women in trait X" can mean any of these:
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Graph A is for traits that are truly different between the sexes; for example, if we're looking at bodily sex (not gender) and we're asking about genitalia, the picture is something like A.  There's a little area in the middle where people are intersex, or have had surgery, etc., but it mostly splits into two groups.
But many traits -- especially traits related to brain, mind, emotions, skills, or identity -- are more like B or C.  Saying "men are different from women in trait T" might mean only that the medians are different, with a significant overlap in the range of values.
It would be interesting to look at a study focusing on transgender and nonbinary people, to see if they have lots of traits that are in that middle purple zone.  I don't know if that study has been done.
The graph comes from the PubMed article you linked to:  Ball et al, "Is it useful to view the brain as a secondary sexual characteristic?", 
Neuroscience and Behavioral Reviews 46 (2014), 628-638.  It's behind a paywall, but I was able to access it through my university's library.