I recently added the JWT on zendesk to authenticate our users, the information about e-mail and name is working but now some our old flow is broken. The flow for unauthenticated users have the option to answer with e-mail out of the box, but the authenticated users do not. Now we have to create a ticket to have this option, take makes the flow wait longer.
Following the picture for unauthenticated users:

authenticated users:

according to the reply that was provided:
The email address of the end user will not be visible in Agent Workspace initially. This is also a limitation that we are actively working to remove. We would encourage businesses who wish to view the user’s email address in Agent Workspace to include this data in the JWT payload in order to prevent future development once this limitation is removed, but it is not necessary.
Also, our product team is currently working on this feature to improve the authentication process but we currently do not have an ETA for an update of this functionality. I would recommend following the article Authenticating end users in messaging for the Web Widget and mobile SDK, to be informed of when this is updated.
I hope that helps. Feel free to reach out to our support if you need further and more granular help.
Best,