Gents,
Whether they're scouting outside or inside the Imperium, it's a given that the IISS is a perfect cover for spooks of all varieties. At any given moment, the IISS is everywhere doing anything making the hoary Purloined Letter ruse all the easier to pull off.
I'm rather surprised that no one's mentioned the Contact & Liaison Office yet.
Here's a group specifically tasked with monitoring planetary cultures and societies in order to facilitate their integration with the Imperium as a whole. C&L is there to spy on and manipulate member planets and the Imperium freely admits it!
Adding to fun, C&L legally operates on worlds that are illegal for Imperial subjects to visit: Red Zones. Depending on the situation, C&L teams may be overt, covert, or a mixture of both. Whatever their status, however, they're still inside Red Zones carrying on the Imperium's business.
Regards,
Bill