You are looking the the 5th meaning:

at some point or degree before a goal or limit aimed at: the shells fell short

The 4th meaning does not apply here if the plane did not actually reach the runway. The plane of course stopped short too, but that was when it hit the rocks instead of the strip they landed short of

Private plane lands short of Charlotte runway

You are looking the the 5th meaning:

at some point or degree before a goal or limit aimed at: the shells fell short

Real life example:

Private plane lands short of Charlotte runway

The 1st meaning only applies to human emotion.

She seemed a little short with me after I cancelled our date

The 4th meaning does not apply here if the plane did not actually reach the runway. The plane of course stopped short too, but that was when it hit the rocks instead of the strip they landed short of