I was on the Lego Inside Tour this year and although they didn't specifically mention the pupils/eyes, they kept stressing how they want everything to be consistent with their products. But TLG has never been consistent because it is a toy that has to evolve and adapt! Over the years we have had: Creator Expert becoming Icons, every changing inclusion of minifigures (exclusive or not) in UCS sets, the brief dabble with Master Builder Series, baseplates vs road plates, adult-orientated sets featuring the black boxes, the list goes on!
I'm not a fan of the new system governing the pupil/eye graphics, I get the logic behind it, but they need to ask themselves "does this look good?"