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I got this working using a service account. It requires you to delegate domain-wide authority to the service account, which requires you to have G Suite. The G Suite admin will need to add the Client ID of the service account with the scope "https://www.googleapis.com/auth/webmasters.readonly".
After the service account is setup correctly, the code mostly worked as-is. I only added the scope and the user the service account is impersonating to the auth process. Compared to the existing quickstart example, I only changed line 2 to
account = searchconsole.authenticate(service_account='client_secrets.json', user_email='[email protected]')
and the experience is identical, obviously excluding the interactive parts.