"Do you think that the copies, the remains of Leonardo's cleaned original, and the restored version of 'the beloved disciple' are very different from each other?"
This writer respectfully suggests - ultimately - it doesn't matter.
I think that, if it didn't matter, no-one would be looking at the subject, so I think that it probably does matter ~ as far as the discussion, etc, is concerned.
I think that the combination of the early copies and the latest restoration probably give an indication of what Leonardo wanted his 'beloved disciple' to look like.
Whether he intended it to be a female, or an effeminate-looking male, I don't know. I don't think that the conclusion is an obvious one, though.
His notes may indicate a male beloved, but his notes also show a typical John ~ which is not like the one in the final painting.
And, if it was meant to be a woman, he was hardly likely to put something heretical in writing.