The two windows with different low-e locations will insulate the same, if they are otherwise similar
There will be a slight difference in SHGC - Solar Heat Gain Coefficient. In other words one will block more free heat from the sun.
If you had the choice you might want to put the one with the low-e on the #2 surface (inside of the exterior glass) on the west because it will reject a bit more of the sun's heat. And the one with the low-e on the #3 surface (outside of the interior glass) on the south because it will accept more of the sun's heat......
There may be a very slight difference in the appearance of the two windows if they were placed side by side.
All in all i wouldn't worry about too much, sounds like you got a good deal to me.