^Again, the word "canon" does not mean "real" or "right" or "what I accept as true." It just means the core body of work. Every Star Trek
episode is part of the canon, part of the core franchise as distinct from derivative works, but it is possible for portions of a canon to be contradicted or ignored by later parts of the canon. Since it's all just pretend anyway, it's possible for a later part to pretend that an earlier part happened differently or didn't happen at all (like TNG from "Datalore" onward claiming that Data didn't use contractions even though he used them constantly up until "Datalore" -- or DS9's version of the Trill ignoring virtually everything that TNG: "The Host" had established about them). "The Alternative Factor" is part of the canon -- part of the central work of the franchise rather than a derivative or tie-in work -- but it's a part whose treatment of antimatter has been consistently ignored and contradicted by everything else in the canon (and that contradicts earlier
episodes' treatment of antimatter). In the same way, "Threshold"'s treatment of transwarp and Star Trek V
's treatment of the ease of travel to the galactic center have been ignored by all subsequent canon.
Canon is not a completely consistent thing. It just pretends to be, even while it tweaks and reinterprets and retcons itself along the way. Which is why
it's such a fundamental mistake of vocabulary to use "canon" to mean "real." It's not the value judgment or the benchmark of consistency that fans mistake it for.