The Baltic Sea Class is a TOS Movie-era Transport/Tug designed to carry large cylinders of cargo (exactly like the ones in the Starfleet Technical Manual). The cylinders quite literally "plug" into the back of the Engineering Hull there. The long extension out the back is actually curved, and serves as a "spine" for the cargo containers.
The "Dauntless" (temporary name) class Mobile Assualt Command Center is a basic Runabout, upscaled about 1.5x the size of a Danube. It features a permanant sensor pod, unlike the replaceable one on the Danubes. The aft compartment has been made into a communications and control center for use to convey orders to assault teams on a planet. The ship usually does this duty while on the planet's surface, usually hidden away. The nacelles help serve as a landing pad, since they are flat bottomed, and the bottom is even with the bottom of the Runabout itself. This creates a much wider landing pad for the bottom of the ship.
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"The things hollow--it goes on forever--and--oh my God!--it's full of stars!" -David Bowman's last transmission back to Earth, 2001: A Space Odyssey
