Not necessarily. A writer may have come along and decided to use the clone if they wanted to touch upon it (more likely if they wanted to use The Jackal). Anything could have happened. We will never know because history didn't play out that way.
Miles was created as a replacement. They had decided to kill Peter over in the Ultimate books and decided they wanted somebody to take over. And, by stunting him over into 616, Marvel have made him redundant because Peter is alive and kicking.And Miles makes Ben Reilly utterly redundant. He's far and away the most successful legacy character Peter has had.
I don't have anything against him, but Miles stood out more for me when he had his own universe to play in. Now he is just another spider-powered hero among a dozen others.