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I've never really thought of all the AP's actually taking place in the same continuity. The ISWG is just a setting with a series of hooks. Some of those hooks are AP's, but we can't play all of them with the same characters. By definition we only play characters who do exceptional things. All those other hooks that we don't play turn out not to be important.
If you're running, e.g., Curse of the Crimson Throne, then Sandpoint is merely a place where a Cathedral burnt down and was rebuilt and Karzoug never woke up, while over in Irrisen Baba Yaga is just late returning because her watch was slow, and Brinewall is just one of several towns in Golarion where there is no mystery: the people simply disappeared. No larger, more sinister story develops in these other places because in your continuity, the problem of the current age is centered around Korvosa.
note there are several APs that reference events in earlier APs. Shattered Star references the first 3 and the two recent cherish ones reference each other in at least rumor.