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Does GDPR mean blockchain based records are illegal? If a user's data is in the blockchain, there is no way to delete it...

Yes but it is personal information about a living person? I doubt it, it's pseudo-anonymous so I believe it is legal under GDPR.

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.