The Jubei story is in all likelihood fiction. IIRC, it comes from the Honcho Bugei Shoden, a compilation of stories about famous samurai that was put out in 1716, some 60 years after his death. As Shinkage-ryu was "o-ryugi", the style of the Shogun, taryu-jiai were forbidden. Yagyu Toshinaga, 20th headmaster of Yagyu Shinkage Ryu, did not believe it, as far as I know.

However, there is a phrase in Shinkage-ryu (perhaps not exclusive to it): "Abara issun" 肋一寸, which means "one inch of the ribs". The implication is that you give the opponent one inch of your ribcage, and in return you take his life.