The study seems to look exclusively at the outcome in the contemporary gene pool. And not at archeological DNA samples, because then the x axis would be in yea

The study seems to look exclusively at the outcome in the contemporary gene pool. And not at archeological DNA samples, because then the x axis would be in years not in generations. There's nothing to compensate for or disregard, the study simply does not claim to describe anything it cannot (very indirectly) see.