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What are the green lights/ports on the dorsal surface, fore of the "conning tower?" Are they launch ports, or am I taking the submarine comparison too far?

Those are Matter/Antimatter pods which supply the AMP cannon and torpedoes. You can see the same pods on any Coalition ship that uses M/AM weaponry, like the Hatchet :



They stick out of the hull because they're designed to either dump the contents overboard via the green glowy vents, or eject the entire pod. Why green? Because reasons.