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And not just him, actually. His (almost) full black sprite is similar to V19 for one reason. Both of them are powerful characters that carries mystery and malice in their development, that's why they have almost the same sprites.
When we talk about mystery and unknown, we come to the most mysterious character in the games: Seth Eyler/UM, which color palette matches Charles, but has different meanings.
UM can be associated with the interpretation of the color black that, too matches power and evil.
Even if UM and Charles are most associated with black, yellow can be predominant to them too. Since both of them are observers in the game. A bright yellow can be associated with "warning" and "alert" which explains why every character possessed by them gets a yellow eye color.
in HC3, when charles first (and last.......) met vincent, his hair is grey, and in HC2, C/Vincent's vessel is white.
let's take a look at his design:
in grey ending (?) vincent's vessel/C appears with brown hair, and the color kinda resembles vincent's hair in heaven's gate.