this is a really interesting question because, like you said, some of them would make sense to see in universe (ariake eyeshadow, shijoumae scar, oosaki eye bags etc) but others would be really... strange. funny to think about funeno dying his eyebrows red every now and then for whatever reason. ooejima fashion fad...?? maybe all of the markings are diegetic but they just appear to be colored normally to those around them. for example... daiba and oosaki both have markings under their eyes which contribute to their visual similarities, but daiba's just appear to be normal eye bags while oosaki's are colored red. in universe it would make sense for them to both have this feature, but oosaki's just resemble daiba's in color. I'm of the opinion that the markings definitely have significance outside of just character design. I wrote an analysis thread about how I feel the red highlights in shiodome's design served to specifically highlight his ears, which contributed to his established motif of see no evil, hear no evil, speak evil. I personally theorize that takeshiba's crime will end up being related to his family's deaths by fire, hence his red markings accentuating his eyes— to indicate that he saw something that had a significant impact on him. so on and so forth. and yes I definitely feel the red eyes are indicative of who in the cast are criminals and who are not. kurosawa is really fond of storytelling through eye color, so the fact that only the side characters have black eyes wasn't lost on me.