Stupid rumour is stupid. The SEGA name is pretty irrelevant in Japan why would MS even do this. Nope.
You are thinking of Sega Mega Drive and Sega Dreamcast only. Sega Saturn sold quite well in Japan, even though it was only on the market for 4 years before it's successor was released, it managed to sell 5.8m units in Japan. That is nearly 4x more than the bestselling Xbox console in Japan, Xbox 360, which sold 1.6m.
Also Sega has several IP's that are fairly popular in Japan, which MS could potentially get as timed Xbox exclusives to help push the system (as well as xCloud) in Japan, including Persona, Yakuza, and Sakura Wars.