The reason they are called "replacements" is because they are designed to completely replace the keycaps on your Filco, QFR, etc. without the need for any special caps. For instance, you can use keycaps from old Cherry boards to replace your modern keycaps, but you will need to find a certain number of additional keycaps (aka moogle kit) to be able to use them with your modern keyboard.
Since they were called "replacements" in the original mass order, the naming convention stuck for subsequent rounds of full set keycap group buys.