It's supremely unlikely that the original settlers to Japan would have made use of none of the local place names. In fact, we'd expect the reverse to be true - that the largest number of toponyms would be found near where the settlers first arrived: Kyushu. This is fairly strong evidence that Jomon Japan itself had a linguistic divide near Nagoya before mainland farmers began colonizing the islands, and that west of there resided one or more now-extinct language families. Possibly on the southern coast east of there as well, for all we know.
Assuming this is the case, and you can get Chinese wet-farming to Japan well before the practice gets to southern Korea, and you can somehow preclude a large Chinese influx.... then whichever group adopted rice-farming would spread and dominate the islands. It's quite possible that the new farmers would even displace the Ainu just as the OTL Yayoi did, or that rice-farming proto-Ainu might drive Kyushan and Shikokuese languages into extinction.
Side note: The Pacific Northwest in North America is probably the closest model to Jomon Japan that exists in a clear historical record. Well-fed societies that could rely so easily on fish, game, and plant protein that resorting to grain had no value. Until it was too late.
