1 No, I don't think Kallis being rated behind Ponting in let's say 2004, was because of of how their respective careers started, because Ponting didn't even have that strong a start to make that impression in the first place. That's an obvious stretch and ignores the fact that Ponting was overwhelmingly more dominant in his peak which created this impression. Ratings normally happen when players hit strong form.
2 I mean, I argue that Ponting was more dominant, and if you want to say higher SR = more dominant, then we agree.
3 Here is where you contradict yourself. Botham started his career faster, Imran did better his towards the latter half, yet Imran is widely seen by peers as ahead.
Yet Kallis who ended stronger than Ponting is not seen as better. Why?
4 Because, as you mentioned, during their peaks, Ponting was seen as more destructive. That is the main difference between them. You can run any sort of alternative counterfactual you like where Kallis' peaks earlier, peer rating for Ponting will still be higher. Because of how Kallis plays.