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I think I read somewhere that in the original ROTJ novelization (which I believe was supposed to be canon, might be wrong and not sure if it still is even if it was), Vader does disappear and Luke does only burn his suit. It’s still possible that it happens off-screen in the film, though I don’t know why they wouldn’t show that and I also think I read somewhere that they originally did intend to. My guess it that perhaps they wanted it to be a surprise when he appears to Luke at the end.
As for Qui-Gon, no clue. Lucas probably didn’t intend for him to be a force ghost when filming TPM, but then he felt compelled to overexplain everything in ROTS so he made Qui-Gon the “original” force ghost Obi-Wan “learned” it from. Which is stupid and takes away from the mysticism of the originals like many other things in the prequels. The whole “I will become more powerful than you can possibly imagine” thing worked better in the originals as it was. And the fact that Vader looked surprised when Obi-Wan disappears means he did not know about this “technique” and it’s doubtful he somehow “learned” it before he died, so it would have made a lot more sense if they just made it a spiritual thing only accessible to the most powerful Jedi with the strongest connection to the force, not something they had to consciously learn.