Yren and Raif each have 7 different eye colours that appear in the game (or will appear).
Canonically, Mylorien chromatophores respond to several things (emotion, strength of the emotion, and even body temperature). So they would likely have a much greater range of colours - for instance "red" would probably vary in intensity and shade depending on the exact circumstance. It might be a more orange-red in some situations, a blood-red in others, and a more violet-red or maroon in other situations.
Logistically, that's really hard to do so there are 7 colours that correspond to a more simple range of emotions and reactions the characters have to things.
Raif, being half-Mylorien, has a slightly more dull spectrum, which can make it harder to discern the exact colour of his eyes. Yren, on the other hand, has very vibrant eyes and even on his smaller sprite, it's typically much easier to tell what he's feeling.
At some point, I switched around what colours responded to what emotions because I was trying to find something easier to remember. Spoiler: I still can't remember most of the colours. Ha ha.
I think they also originally only had five colours and I expanded it at the same time I changed the system.