I’ve always thought that, through the force, Luke recognized the voice calling to him as his fathers. He looks and sounds startled and surprised. Then when Vader continues, Luke realizes who it is, causing his apparent sadness and feeling betrayed by Ben.
But I agree that it makes Yoda’s reveal in Jedi redundant. But Han and Leia confess love for each other in Empire, then in Jedi it’s like that didn’t happen. So maybe it’s another problem to fix in Jedi (the broken movie) instead of Empire (the best one)? I dunno.
It’s not really a big deal to me that Luke still wants confirmation from Ben and Yoda though. It could be Vader playin’ Head Games. And Luke can’t take it anymore.