I never thought it was some dark side thing. Luke is mysterious because the Jedi are mysterious. They walk around with robes and hoods and are are mystical and solemn, like monks. That's also the reason he has the black uniform--its supposed to be "jedi-like", in Lucas' words. The reveal of Luke in darkness is a great re-introduction to him in his new calling, completing his new lightsaber to boot. And then when he turns it on--you know that he's going to kick Jabbas ass. I guess its the "return of the jedi"?
Anyway if Hamill swears that he never shot it than maybe he never shot it. It could easily be a double since you don't see his full face. It looks like Hamill's face to me, but that could mean they just had a good double.
What surprises me is the meditation chamber of Vader's. Did they re-build that whole set just for one single shot? Normally that would be possible, but given how cheap Lucas is about not having to build sets this surprised me. Maybe they had it in storage, but it doesn't seem like one of those props/setpieces they would hold on to. I'm wondering if this was an outtake from ESB, but then I can't imagine where in the film it would have fit if it was. The dollying-in towards Vader seems very characteristic of Kershner, but very out of place for Lucas and Marquand.
Also, the Vader dialogue DOES sound like ROTJ-era Vader. But the pieces sound like they are probably alternate recordings for ESB.
Luke, join me on the darkside (and I will complete your training).
My son, (come with me, it is the only way).
And so on. He also says "Luke" a bunch of times in ESB, but not in ROTJ, which may be where they got the Luke line from.
But if the scene was basically finished why would they drop in these constructed readings? Baronlando has a good point about making things overexplained, but the scene was supposed to have Vader communicating to Luke telepathically like in ESB, and not only would not that not be clear at all without the dialogue, I would think you would want to have dialogue for this to even be possible. So, it's weird if the scene was finished and always had dialogue that Jones never recorded original stuff for it. Maybe this is it, I dunno. As I said, it does sound like Jedi-era Vader, even if the lines seem suspiciously like ESB alternates.