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It has never been mentioned that the EMS affects chakra. Only the ability to not lose sight thus far. Sasuke was able to manipulate amaterasu with just an MS.
Its obvious that EMS affects the chakra, for example when sasuke fought danzou he could barely maintain a regular susanoo. But when we see sasuke fighting kabuto he was able to instantly enter his full susanoo form and use amaterasu at a large scale without showing any sign of fatigue. If MS sasuke fought kabuto he wouldnt last 5 minutes because by then his susanoo would exhaust him