Short Answer: Yes.
Note that in Alpha Strike, any unit attacking an aerospace that is within 2" of the aerospace unit's flight path is at Short range. That replaced the Quick Strike "if you are attacked by an aerospace" rule. Since Strike and Strafing attacks require the aerospace unit to attack a target within their flight path, this rule effectively includes the "if you are attacked by an aerospace" rule plus some.
So if you are attacked by an aero (with a Strike or Strafe), you are within the flight path and therefore when you attack back you are within 2" of the aerospace unit's flight path. You are therefore at Short range, and instead of the standard +0 short range modifier, you use the Short-Range Targeting's adjust short range modifier of -1.
