See , he is just beginning so he is careful. Yes it will affect his pace (of the wicket) but won't affect much his speed (from the hand)
After his comeback to Pakistan team after few months you will see that only his entire foot will be behind the line but not as far behind as of now.
Amir's runup has still got same rhythm and also his hand speed is quick. If you have seen bpl than Amir along with Sami and Fidel is the quickest uptil now but not as quick as he was before due to one thing :
In m opinion he has needlessly shortened his runup by 3,4 steps. He needs to revert back to old runup sooner than later than he will bowl 5 to 8 km faster than what he is bowling now.
With such a small runup he cannot bowl many bowls between 145 to 153kph which he is still capable of bowling.
I don't mind him bowling so back from the bowling crease ( for the time being ) but my concern is his runup length. It was perfect in 2010 . It wasn't very long it wasn't very short and it gave him enough momentum to bowl fast.
Alhamdoulillah he still has got the ability of hitting the lengths he wants , swinging the ball , reading batsman and setting up a batsman. Misbah is 42 but it is no mean feat getting Misbah out bowled of a yorker.
So nothing much to worry off. He still is an asset MashaAllah.