The glowing aiming dot for head shotting the Atlas was not.
The cockpit for an Atlas is in the eye. When they glowed they were MUCH easier to head shot since the glow gave a perfect aiming point ... as long as you could remember which eye held the cockpit.

That was the reason it was removed ... it was actually a significant disadvantage to the Atlas to have glowing eyes. Odd how folks seem to forget this and simply reminisce over how cool it looked.