Scale and Size are intentionally different things. A Size 3 enemy will have the same Toughness and such regardless of its Scale. Basically it was just a simple way to say "It's time to get in the Giant Robots" that sentai really popularized.
In short, Size does not equal Scale. Scale has zero mechanical weight EXCEPT when comparing it to the Scale of other creatures. Giant Scale threats can hit Hero Scale characters, but Hero Scale characters cannot deal damage to Giant Scale Threats. That's it.
Does that help?