The text says Sai Baba 'left the body', but also that he is beyond death. Can you explain this apparent contradiction?

This is not a contradiction but a description of a Yogi's profound spiritual state. Chapter 43 explains that Sai Baba is the 'complete Supreme Brahman' for whom the concepts of birth and death are irrelevant, as the world itself is an illusion from the standpoint of Brahman. His departure was not a death in the ordinary sense but a voluntary act, a 'spontaneous play of Yoga for the sake of the devotees’ salvation.' He chose to 'burn the body in the fire of Yoga' and 'merged himself into the unmanifest.' Therefore, his leaving the body was a conscious transition back to his unmanifest state, not a perishing. As Chapter 43 clarifies, he remains eternally present in the hearts of his devotees.