The Spec Ops ID is primary used to on ships who have equipment and ships that break the technology usage rules. They are also used when another ID doesn't fit with the role play of the character due to restrictions on the ID they would normally use.
I believe Doc's Med.Force.One has a Spec Op ID, which makes sense. Seeing as his ship is a medical vessel that can be called upon by almost anyone (save for the Gallic Royals). If say, the government of Liberty called upon him for some reason, with a ZG ID, he couldn't dock in 90% of Liberty. Which doesn't make sense with the role play of the ship.
Just my thoughts in regards to Doc's stuff. I can't be sure though.
Theres a spyglass named "Metropolis" rolling around with a Spec Ops ID - ran into it once, was probably the most interesting experience I had. Negotiating secret deals, literally seconds before an ion storm.
Maelstrom is a Liberty Rogue Scylla destroyer class vessel under control of the Junker Evangeline McDowell, leader of a violent separatist group known as the McDowell Company. It serves as the flagship of the militant sub-faction which lives within the underbelly of Liberty and her surrounding territories.