Is it possible for the Internet Agent or the post office / domain to mark messages as external for instance in the subject line so that users know that the email came from outside of groupwise?
GWIA itself won't do this. I normally configure the frontside instance (i.e. firewall) to do so or at least add some sort of x-flag which a rule could act upon.
You can also create a rule like "item type is mail / view name is "internet" / subject contains <anything>" which should identify stuff coming in via GWIA. You won't be able to modify the subject, but you could add a category to colour the message up.
That's why i usually prefer to let the perimeter device routing external stuff to the GWIA set some sort of funny x-flag (i invent a special unique fantasy name for every customer) to react upon in the rule. There are some many internal things sending logs / alerts / whatsoever to GWIA which you normally don't want to get flagged as "dangerous internet mail".
If you mean "can a rule act upon a custom x-field?" the answer is "yes, absolutely". It must have a value, though. So you tell the FW to add e.g. "X-nonsense=Windows10" to any incoming stuff handed over to GWIA and let a GW rule upon ""X-nonsense" contains "Windows"".