Most Halo players don't know about the different kinds of Spartans, don't care about the different kinds of Spartans, and don't care to know about the different kinds of Spartans. Introducing the not-as-good Spartans as Spartans would just confuse people, which is why I don't believe they are supposed to be III's.
The best way Bungie can attempt to avoid discontinuity with the supposedly canon novels is to avoid their subject matter entirely. Subtle nods are okay, but nobody should have to know any of that crap to enjoy a Halo game.
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