If the Jomon DNA of Japanese men is found more in the Y chromosome, wouldn’t that indicate that Jomon men were reproducing quite successfully, and their male children were being preserved? Maybe Jomon men were living in more isolated places and kidnapping Yayoi females? Or perhaps they were successful in fighting and capturing Yayoi females? Maybe the Yayoi females found this Jomon men particularly attractive?
That's where it persisted, but the percentage of modern Japanese who have looks pretty good, considering how long it's been.