That's pretty much what I'm saying. JJ Hagoromo is stronger than Kaguya. Pre-JJ Hagoromo is obviously weaker than Kaguya. Should have probably made that clear. Kaguya's base power should be around the level of the 100% Juubi.
Taking the Chakra from all Shinobi increased her chakra beyond that. So, Naruto and Sasuke didn't actually fight her base power, but a powered up version of Kaguya.
Again, that's not entirely true. Black Zetsu even said she become stronger after taking more of Shinobi's chakra:
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Taking chakra make her stronger, not return her to former self.
Remember, the Juubi was attacking Hagoromo and his brother to get it's chakra back. This is before Hagoromo became the Jinchuriki. That part doesn't make sense because their chakra shouldn't be Kaguya's.