heinrix only allows the rogue trader close enough to see that subtle difference in the color of his eyes after kiava gamma. it's a conversation he puts off until the completion of his mission, putting his professional obligations over his personal desires.
it's only then, when he allows himself that closeness, too, that the rogue trader notices it.
and he only reveals why his eyes are like that later, after he's been rescued from torture in the depths of commorragh - when he's weak, when he's vulnerable. (he doesn't want to be seen when he's like that, either - he hides himself away while he tries to heal his injuries.) he tells the rogue trader how he lost his eye, how he saw himself afterwards (as a "maimed freak") and how he took great pains to regrow it - and why.
when calcazar recruited heinrix, he had heinrix remove the implants that marked him as a psyker because it made heinrix more useful as an agent. heinrix chose to regrew his eye for the same reason - he considers himself less a person than a tool of the inquisition, and one who should repay the mercy of being allowed to live with whatever suffering makes him useful.
but he is, in his own view, still flawed. he can say as much after rykad minoris.
and even though he considers it a weakness, a part of him still wants to show that weakness. tanakia, his fellow acolyte, can even call him out on it.
it took him years to regrow his eye. but even though it doesn't quite match, he'll allow the rogue trader close enough to see it - to see him. and he's still trying to drown that desire for compassion and mercy buried deep inside his soul - but he'll let the rogue trader close enough to see that flaw, too. maybe they'll accept it. maybe they'll even encourage him to show it.
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