If the two aircraft are experiencing the same TAS, and the same wind, and travelling in the same direction, they will cover the same distance over the ground in the same time.
TAS + Wind = Groundspeed
These are all vectors, of course.
That said, the indicated (and calibrated etc) airspeed of the aircraft at high altitude will be significantly less than that of the lower aircraft. This is a measure of the dynamic pressure the aircraft experiences as it passes through the air, which in turn is a function of the density of said air, and the square of the velocity. The density of air at 40000 feet is significantly less than density lower down, hence the difference. This dynamic pressure is also an indication of the sort of energy state the aircraft is in, and the sort of flight regime that would be encountered. The lower IAS (or "Q") means lesser control response, higher angle of attack, and less power available, for example.
In reality, the reduction in the speed of sound with temperature means transonic effects complicate the matter somewhat at high altitudes. Also, in reality, if we are considering identical aircraft, I would imagine it would be pretty difficult to achieve the same TAS at 1000ft as at 40000ft without:
a) Ripping the wings off at 1000ft because of the excessive IAS/Q as mentioned, or
b) Being unable to maintain altitude at 40000ft because of the insufficient lift because of the low IAS (or, in seeking sufficient lift, exceeding the critical angle of attack and stalling).
Sadly it is too early in my career to have experienced flight above 10000ft, however its not very long ago I was in the classroom getting my head around this stuff, and this is how I would explain it to myself.
Objections/comments/criticism welcomed!