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It's the former.

> why is knowing whether an unidentifiable reader is accessing a website via Incognito mode a privacy issue?

Because it makes Incognito less useful, and Incognito is a tool for people to control their privacy.

Anyway, Incognito isn't only used for anonymous browsing. For example, a user might use an Incognito window to register on a shopping site, providing all their personal details, just because they don't want Facebook to see their activity on this third party site (and they don't want to bother signing out of Facebook in their main browser context). So it's reasonable to consider "is using Incognito mode" to be private information.