No, but I didn't get to them yet. Ideally all commanders, leaders, engineers etc. would have little distinguishing features to let us tell them apart.
But Sectoid Commanders
do have a little distinguishing feature, unlike leaders, engineers, etc. About as big as a naked Sectoid can have. That's why I asked.
How do you even know eye color is relevant in a mod where some creatures all share the same model and others (like humans for example) have multiple models for the same unit type.
Me personally? Because I a) explore the shit out of the mod's data and b) notice that pretty much all the cases with multiple models amount to either a direct hair/clothes colour swap or are treated separately for research purposes. Red Dawn pioneers? Separate research for males and females. Black Lotus Hosts? Dye their hair. Syndicate Supersoldiers? Swap camo colours. Well, okay, the last I didn't notice until recently because I use Michelin Men.
And there are quite a few units where ranks have subtle differences. Syndicate Mercs from above, red vs plain Floaters, Hybrids with small but differently coloured shoulder pads; Machinobis and Assassins, for an extreme example. So I've learned to be careful, or just stun the lot and sort it out in research for future reference.
I don't really know which human faction you're referring to that has
significantly different sprites for a singular unit that's not telegraphed in some way.
I do get where you're coming from, and my Sectoids have the circlets filter down to leaders, plus separate inventory sprites for non-soldiers and another one for engineers. Hybrids with sprites pilfered from Piratez that are more than just a colour swap. BL Warriors with sprites distinct from ninjas. Etc. But quite a few are still subtle, and I like that.
Scorpoids are a somewhat excessive case since they kinda blur into the surrounding cave terrain at the best of times, and can frequently have their backs turned so the eyes only stand out when you middle-click them. So the chiefs having at least some sort of distinct ceremonial weapon would be nice. Although when they actually face you, the laser eyes do stand out to me, three pixels or not.