@Neil - Say I have 2 PM's managing cases. I have logic to alternate case assignment to either PM.
I have coded my plugin to auto-respond to a new contact using a From address of a case PM's email address. So the contact would not receive an email from system@myco.com but rather john@myco.com.
When the contact responds to the email that was autogenerated by the system with a From address of john@myco.com the contact's email will go directly to john@myco.com which will bypass the email router configured for system@myco.com.
Therefore, it seems like I'll need to rely on the users to configure their Outlook settings to sync their emails back into CRM to handle proper case activity association. I'm guessing this is a fairly standard scenario for CRM implementations?