The news about Amir Khan is not confitmed. He has given script but it's not official that he will be part of Dhoom 3
Nobody knows what script Yash Chopra gave to Aamir. It could also be the script that Yash Chopra might direct for his next venture (Remember, Yash Chopra announced that he is getting back to direction by the end of this year?). I am not sure if Yash Chopra will go back to Shahrukh again for his next film (there have been quite a few rumors that there is some problem between Yash Raj Films and SRK).
And also, Dhoom Series is a film handled by Aditya Chopra and directed by someone else. Why would Yash Chopra take the script of Dhoom-3 and deliver it to Aamir? The producer is Aditya Chopra, the director is someone else (or maybe Adi himself). Yash Chopra doesnt interfere in films that are not directed or directly produced by him. He leaves it to Adi.