I don't see the correlation or contradiction with the underlined parts. There wasn't a part of Naruto that was left behind in those previous dimensions, so there wasn't an instance of a single cell possessing Naruto's chakra being left behind. If part of Naruto was left behind in a previous dimension, those two lines would contradict. But that isn't the case here.
The bolded parts are two separate instances that aren't connected with one another. In one instance, Madara was bisected and half his body was left in the real world, which still had some of his chakra. In another instance, half of Madara's body was left behind after Kaguya was revived and was most likely devoid of his chakra, as I stated before, since Kaguya was absorbing the chakra of everyone. In the first instance, there wasn't anyone absorbing chakra. There's no contradiction there.
If Madara's lower half had sufficient chakra to sustain the TSBs, then they would not have disappeared after Kaguya took over. The lower half was confirmed to contain chakra as that is how Hagoromo was able to appear in the physical world.
The lower half may have contained Hagoromo's chakra, which is how Hagoromo manifested himself. It was already said Hagoromo's chakra was needed to awaken the Rinnegan, which means Madara did have it. But that doesn't necessarily mean some of Madara's chakra was also left in that half of his body, which explains why the gudoudama disintegrated after Kaguya left into another dimension.
In case this is somehow still too hard to follow:
Kaguya absorbed Madara's chakra.
Kaguya left to lava dimension
Madara's gudoudama disintegrated.
Madara also was not dead while Kaguya was alive.