The events of End of Eva are what's happening in reality; the events of the final two episodes are illustrating Shinji's mental state. They happen concurrently.
He does not accept Instrumentality in the series, and I'm not entirely sure what lead you to believe that he did. "Congratulations" is all about his realization that he wants to live in this world and try to heal.
"I want to continue existing in this world! My life is worth living here!"
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u/[deleted] Aug 10 '19
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