I'd rather a future possibility be having the option to change the Alloy colours to your liking in the Hangar after having purchased them, but have it not remove the extra 3% boosts so it'd be more of a cosmetic change than a power change.
So buying Antimatter would let you choose between Ion/Fusion/Antimatter for example, but if you've only bought up to Fusion then you can only choose between Ion/Fusion to keep that "reason to buy" in there for the Devs side of things.
This way Remnants can stay with their current Alloy variant and pilots can adapt if they choose to.