I don't think the Antagonist in the Prestige is Borden (the IC) either.
"Like The Shawshank Redemption and The Fugitive, The Prestige centers conflict in the Overall Story Throughline around the unjust imprisonment of an innocent man. This imbalance in the UNIVERSE separates Borden from his wife and child, Angier from the secret he longs to unravel, and everyone from the peace that results when the scales of justice balance out. Tit-for-tat. ”Abracadabra” and a well-placed flintlock shot deliver the parity needed to resolve the story’s central inequity."
Since Borden is the one being unjustly imprisoned, and him shooting Angier (the MC) resolves the Overall Story, it seems more like Borden is the Protagonist, or at least illustrates one or more of the Protagonist Elements.
Thanks for the great list though!