The current writing staffs on the current Trek shows might consider the Khan audio canon, but when they leave and new writers take over, they will be under no obligation to do so.
Which is always true of canon, even onscreen canon. ST V showed the Enterprise getting to the center of the galaxy in a matter of minutes (the dialogue said 6.7 hours, but there were about 20 minutes of continuous action with no room for a time jump), but DS9 and VGR ignored that and based their entire series concepts on the premise that any such journey would take decades (and TNG ignored it too in episodes like "The Price" and "The Nth Degree"). Those creators pretty much considered ST V apocryphal, but their successors on SNW acknowledged Sybok. Then there's VGR: "Threshold," an episode so infamous that its own writers declared it non-canonical -- but Lower Decks acknowledged it anyway. Different creators make different choices about what parts of a series's past to acknowledge or disregard.
I've said before, one of the biggest misconceptions about canon is that it's binding on the primary creators of the work. It's the other way around -- whatever the creators decide to establish is automatically the canon by definition, even if it changes or disregards earlier canon. Creators generally prefer to stay consistent with past continuity, yes, but nobody forces them to, because they're the ones making those decisions.