Kaguya having more Chakra than Madara is irrelevant, as Chakra isn't the deciding factor; unless we're saying P1 Naruto is on a completely different level than Kakashi. Now that has been established, we can establish how Madara shit stomps her:
Madara having the 3rd eye enables him to teleport like Kaguya. Even if not faster than Sasuke, he possess the Rikudou Senjutsu; so he will be able to sense when the portal is being opened, and dodge it as Naruto did. There is the fact that she can't do anything to Limbo clones. Only Hagoromo's Chakra can harm it, and Kaguya doesn't have his Chakra. She will be pounded by them. Madara can also absorb techniques like Kaguya through Preta path, so that is also pointless. Madara can throw Asura rockets through portals, attacking Kaguya through surprise attacks. Once she is weakened, Madara seals her with the moon and sun; both Jutsu he stated to wield in one body. Madara takes this comfortably. If Naruto and Sasuke were pushing to her limits; and both of them were getting stomped by Madara, then Madara will do worse.