In probing - they would be placing probes into different holes of the human body. Nose, ears, butt, p**is or va**na, mouth & they would definitely visibly see Male & Female reproductive organs.
In that advanced of a society - they would likely have an understanding of microscopic technologies - far superior to our own microscopic technologies.
If we can classify XX & XY chromosomes - it is safe to assume they would also be able to identify those characteristics. They would also likely have X Ray technologies - which would have them pondering why this biological male - has silicone based additions to their chest to make them appear to be a female when they aren't...