Does the Colony MotherShip link to the underbelly of the Havester as the City Destroyers did to the Colony MotherShip?

Sort of. In the book version when the sphere is using holograms to explain the history of the harvesters David notices that the colony mothership “buds out” of the Queens ship similar to giving birth and he ponders how many thousands of colony ships could have come from this 1 queen.  It explains in greater detail how all of their technology is grown. It also explains that they’ve been doing this for a loooooong time and there are entire galaxies that they’ve stripped clean before they got to us and they are the reason that outer space is so quiet. Also, spoiler alert if it remains cannon and they do a part 3 but the sphere created the harvesters at some point in the past