I don't think the Japanese entity and US entity have any relation to each other anymore. I think US entity divested itself of Yahoo Japan completely in 2018 or so. Yahoo Japan is now collectively owned by Softbank and Naver under some holding company (it was big news in Japan when the merger happened).
Legally being placed under the same corporate entity was a while ago. As is normal for big acquisitions, actually merging the businesses is a much slower process (allegedly part of the reasons BA's first days of operating at Heathrow Terminal 5 were a mess is that it was the first time BEA and BOAC were actually working together).
My point is just, from what I've heard the switch to Line Yahoo reflects a real integration of the businesses, not just a change of brand.