Apparently decals are controlled by the "Shader" quality level. Anything above "low" shows the decals.
Doesn't fix the problem but it's good to know. Maybe I can alter some quality on the skin texture so that decals don't show up? Now that I can texture the skins properly I'd rather do that and have control.
decal_terran01_01.dds is the default. If you take this, color the alpha channel completely black, and reupload with the same name you can make it transparent.
Still can't give individual units different decals, but this allows for customization because you can now take off the decal then skin the texture for a new model.
Update again: Apparently you can replace Raynor's Raider's but you no matter what decals I replace, default (terran) and the default texture remains with the same logo. I have no idea where it gets it from since I replaced all the ones like that.