Board Thread:Theories and Speculation/@comment-5413572-20150114180437/@comment-5413572-20150114192723

As far as my theory is concerned, Kaguya originally had the Tenseigan, and thus had the Byakugan as well. However, because Black Zetsu was using Madara's body to rebuild Kaguya's, her new body was thus based on both her original form and the "material" provided by Madara's biomass. So, since Kaguya had the Rinne Sharingan and Madara had managed to awaken it, her new body had it fully intact. However, since she had the Tenseigan, but Madara had no Hyuga chakra/DNA, her new body couldn't fully replicate her Tenseigan, and was forced to compensate with a default Byakugan.