Here is some facts. Assuming always.

in OT we have a dude with a mask, never see his eyes and an old lady with yellow eyes. Both their face are white/gray and damaged/deformed. Assuming have an old lady palpatine with yellow eyes it could make contrast with his weak appearance.

In PT we have a tattoo guy, a droid general and a fallen jedi plus anakin.

Maul has evil orange red eyes that complete his appereance as...evil.

then we have dooku that got nothing. and GG that is a lizard cat eyed creature.

Now we got explained by PT that the "masks" have fall from palpatine's face and now he cant hide it anymore.

Mixing up an element that was not used properly even its from bad script of from visuals yes it might cause confusion. And again we dont know what a "zabraak species" is. Taking reference from games that was set on something wrong its naturally it will cause confusion and debates

A solution is that only palps can have the eyes before and after his transformation, or add partial hits of sith eyes here and there to all the bad guys. A bit of evil something that gains someone when is in rage.. Yes you can make the difference adding the sith eyes to known jedi puting the dilema who is good after all. Or may have them indeed keepers of the peace and never fall into darkness.(aka blade runner you never know)

Or indeed dooku for example can get a desaturation/pale tone to show that he is a "sith". Anakin too.

As i said before each editor sets its own rules and aesthetics to their edits. It might be star wars-y or not. which defies all the above sayings ;)

-Angel