Starting in Winter 21, Salesforce introduced a new enhancement for standard Email-to-Case where incoming emails are matched to existing cases based on the Message Id found in email headers instead of the Thread Id included in the Subject/Body of the email. https://releasenotes.docs.salesforce.com/en-us/winter21/release-notes/rn_email_to_case.htm
This change was made specifically for standard Email-to-Case, and doesn't directly impact the behavior of Email to Case Premium. That being said, we understood how this functionality could also be beneficial for Email to Case Premium customers.
Starting in version 6.43, Email to Case Premium was updated to store the Message Id of incoming emails, and will look for matching Message Ids on future incoming emails. If a match is found, whether or not the Thread Id is present, the email will be successfully added to the existing case.
This change to Email to Case Premium will specifically solve for the situation where someone sends in an email to create a case, copying their colleague(s), and a colleague replies all to that email. In the past, this would create an unwanted duplicate case because a Thread Id was not found on the colleague's reply. But now, Email to Case Premium will match the colleague's reply to the original case based on the Message Id match.
At this time, the primary difference between standard Email-to-Case and Email to Case Premium is that Email to Case Premium is unable to capture Message Ids on emails sent out from Salesforce. This is currently a Salesforce limitation.
As such, Email to Case Premium still relies on the presence of the Thread Id for ongoing case correspondence. Email to Case Premium packages its own custom Thread Id field, and customers should continue to utilize this field in email templates used for case correspondence.
Additional Considerations on this change being made by Salesforce can be found here: https://help.salesforce.com/articleView?id=000355168&type=1&mode=1
One important consideration to note is that the new threading behavior will not be supported in emails sent via automation (such as Workflow, Process Builder or Flow). Responses to emails sent from automation will always result in new case creation, which may be undesirable.