Most scholars agree that by around 40,000 BC glaciation had connected the Japanese islands with the Asian mainland

I'm not sure about this. Wikipedia has a map that makes it clear that Honshu-Shikoku-Kyushu was not directly connected to the mainland, but it makes it unclear whether these islands were joined to Hokkaido (which was). The fact that the Tsugaru Strait is a major biogeographic boundary suggests not. OTOH I find several non-academic sources online claiming that all the major Japanese islands were connected to the mainland. Maybe the map wikipedia uses is wrong.