Both of my previous (and future) texture/character packs have no brows painted on the face texture, they are added using the Upper Eyebrow mesh, which can easily be swapped out via MAT files - the appropriate upper eyebrow texture area on the face texture is filled in with some brow texture, but the trans maps and material color settings do most of the work. I'm not sure if I understand your proposed method ("...rather than a transparency for a little more realism"), but it sounds like you plan to include a ton of (face) texture maps with the different colors... if that's the case, I'd recommend against doing that ;).

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