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Certificate Transparency logs contain personal information about a few people right now. Is that legal?

Yes, but can only be used to contact to certificate authors about certificate-related matters.

You're wrong, just search for ESTEID in the logs.

EstEID is a purpose-built identifier. They are subject to a different law.

How is a purpose-built identifier uploaded without explicit consent somehow not subject to GDPR?

Yes but you consented to that.

No I haven't, but someone else has submitted a few certificates of other people. Search for ESTEID in the logs.