That document doesn't mention anything about Airplane mode at all. Nor does it describe the Significant Locations feature as "saving the list of wifi access points"; in fact, I'm fairly sure that's not what they're talking about, and instead they're talking about the feature iOS uses to determine that you tend to go to the same place for lunch on Tuesdays or the same friend's house on Saturday afternoons and offer that as a Siri suggestion -- which is almost certainly GPS-based.

Last but not least, Significant Locations data is not just described as "end-to-end encrypted and cannot be read by Apple", it's clearly in the list of items under "By enabling Location Services, location-based system services such as these will also be enabled": e.g., if you're really, really bothered by this, you can turn it off.