Board Thread:Theories and Speculation/@comment-27260817-20160203170532/@comment-734582-20160204174534

Georgio722 wrote: Six Paths Sage Mode has the Rinnegan marking, and All Tailed Beast Chakra Mode has the nine magatama marking, and since Naruto didn't have either after Kaguya battle, then there can only be two options: Sage Mode & Nine-Tails Chakra Mode, or Sage Mode & Kurama Mode

As for not having the Toad eye marking, maybe Naruto mastered the Toad Sage Mode, where the markings disappear or something. Or, since Naruto doesn't have Hagoromo's chakra anymore (or the chakra of the other tailed beasts) and so the markings disappear and what we see is what Elveonora said.