TL;DR:
My edited pattern has mystery splotches and random markings as the "secondary color" // Secondary color alludes me // Can't export png files with secondary color option.

I've got the models and skins working fine, my question is more related to how the pattern texture is read by the game itself.
I am designing skins using Blender, and making more specific changes using Paint Tool SAI, which has been working a charm for regular skins, but there is something fundamental I'm not understanding about patterns - initially when looking into the example textures given, I was under the impression that the patterns were read using the black and white textures to differentiate between secondary and tertiary colors, but that's definitely not how it's working in the game.

The example pattern given, 'onfe_faelain', loads okay, although when comparing the two png's, I don't seem to be able to tell where the "secondary color" on 'onfe_faelain' actually is - There's a secondary color mask over the eyes in 'onfe_faelain' that I can't seem to spot when looking at the texture file.
I ran an eraser tool through the right eye and saved the new pattern texture, only to find that png has completely broken as well.

Comparatively, when loading my pattern in game, there's splotches and brush strokes on the character that don't (shouldn't) even exist in the texture file itself.

Happy to share screenshots or the mod files if what I'm explaining doesn't make sense, but I've been stuck for a while now with these phantom brush strokes appearing in game, been reading the documentation and using trial and error to try and find out what's gone wrong, but nothing has lead to an answer or solution yet.