While it is a fascinating question, i dont believe the beis yosef would never have asked it if he was around today. If you look in the migillas taanis (written during the time of the gemara by amora’im), the reason that it gives for chanuka has nothing to do with the miracle of the candles but rather the chunukas hamizbeach.
So why did the beis yosef ask his question? Did he not know about the migillas taanis?
The answer is probably no, he did not know about it because he didnt have access to the manuscript.