That's exactly what I thought when I saw it. It's confusing, and although it's probably not the intention of the writers, I feel like the character of Joe Pendleton did in fact die.
That bothered me when it came out and it bothers me now after watching it again. At the end, he doesn't have his body, or his memories. He's dead.
And even if you try to make it work inside the premise of the story, and he's not dead, where is he? Is he in heaven? No, he's not due there for another 50 years, right?
And what about Tom Jarrett? We're supposed to think Betty will fall in love with him. But he's not Joe. He doesn't have Joe's personality. And for that matter, he doesn't have Farnsworth's body (the one that Betty knows). So why would she fall in love with him?
I have to admit, if he did remember his life at the end, the ending would have a completely different effect. More realistic, if you know what I mean, but maybe less poetic, or mystical, or whatever you call it.
Oh well. Enough griping. Still an excellent film. "I choose to think there is no free will..."