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Yes, the standard functionality on the web portal will work with custom email templates as per standard ones.
You have to set the flag "Can unsubscribe" in the mail template.
All of these templates are then shown in the web portal under "My Profile -> Mail Subscriptions" - if you deactivate the delivery of a specific mail template from there, an entry in DialogMailNoSubscription will be created.
Restriction of this feature: It works for SendRichMail jobs only - not for SendMail.