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> The only real issue I can see here are users who have registered their own domain under an eTLD

Doesn't the differential privacy system described above prevent even that from being an issue?

I'm not sure if they're planning on collecting every homepage domain here, or just asking something like "Is your homepage domain in the list of top 1000 domains?". In the former case, just having the domain listed could leak information. In the latter case, I can't see any issues.

It's more like: "Is your homepage google.com? Flip a coin, if it's heads tell me the truth, otherwise flip another coin and answer yes if it's heads or no if it's tails." (A bit simplified, but that's the general idea behind differential privacy.)

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