I guess we’ll have to see how the system plays out in the end, but as it is now, with one loadout card that determines your merc skin, augments, weapons and even weapon skins (if I go by your not-so-subtle hint…), it’s going to be all about compromises. I think compromises are fine for the gameplay aspects (weapons + augments) for balance reasons, but I don’t see why you would have to make compromise on cosmetics a well… 
I’m really hoping to see a mechanism that allows us to combine the cosmetics we prefer with the weapon + augments loadout of our choice, either by assigning multiple loadout cards to the same merc or through some sort of crafting to combine parts from multiple loadout cards into one.