Tracking Tokens and Smart Match is set up in Email configuration. While "Reply all" function replies in the same thread as it should, my PowerAutomate flow doesn't reply in the same thread. Eventhough I'm passing the Tracking token, same Subject, To and From in the flow. 

As an alternative I tried using the PowerAutomate 'Reply to Email' Action and an Outlook Trigger to run the flow. Trigger can't be used for all mail boxes in the tenant, but only for the one in the connection reference.

I logged this as a support Ticket and was recommended to report a limitation here.