Rinnegan eyes could still disrupt the chakra of Kakashi who (although transplanted) uses Mangeyko sharingan. This gives me reasonable belief that the Rinnegan over powers the Sharingan in regards to the which has "priority" when there moves class such as Amaterasu vs Shinra Tensei, Id say ST will still reflect it. Rinnegan also allows Nagato/pain to attack/extract spirits of people, which pretty much makes Madara's intangibility a nonfactor.
well danzo doesnt have it, hes got shusui's eye. Madara himself stated he wanted Nagato to use the Outer Path: Samsara of Heavenly Life Technique on him implying he can die or will die and required revivement = not true immortality. That being said it shows Madara's vulnerability to that ability showing the king of hell that Pain/Nagato summons to give/take souls effects Madara. The time space jutsu is very similiar to summons in the way it works. That being said it can roughly be compared to nagato's animal path that can summon the other pains (and one can assume that Nagato himself has all the pains abilities to a greater extent).
EDIT: SORRY THERE MAY BE A SPOILER IN THAT DONT READ IT IF U HAVENT READ THE CURRENT ISSUES!!!!!