Naruto said he kept the Kyuubi's chakra in a separate place than his own, and he gave the Alliance the Kyuubi's chakra. Where do the traces of Naruto's chakra come from then?
Also the Shinju that absorbed Naruto's chakra, which was summoned by Obito, was cut down by Naruto and absorbed into Madara.
It makes no difference if Kaguya had a portion of Naruto's chakra, since she was warping them all into different dimensions at the same time. The only exceptions being when she traveled into a different dimension temporarily and came back out in a different spot, but that still changes nothing.