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Do we care about the trillions of bacteria cells and such living and dying inside our bodies? In practice we're busy with what we're doing and are so much larger and more complex than them we don't really spare them any thought or ethical consideration.

I feel it's similar with the Emperor. He's now become millions of times more complex and powerful than he was, though gradual accretion of souls and belief and actually god-like. A lot of his old humnaity seems to have been lost in the process and he probably doesn't care about individual humans much but overall he's still trying to oppose the chaos gods and defend humanity as a whole.