To use planetary resources you have to set up mining, processing and industrial facilities first - but to set up the facilities you need the resources first. Ops! That's why you need to dismantle the ship: to use its resources for a jumpstart.
That doesn't quite make sense. To set up mining, processing, and industrial facilities, you need construction machines and raw materials: the machines are brought on the ship with you ahead of time, the resources come from the planet. A very dumbed-down example is Starcraft's SRVs being used to mine crystals to then build whatever you need. You don't take the Hyperion and dismantle it for parts and pieces to make your base, you build things using the crystals. (The game provides you with a free initial base because it's easier to get the game going and prevents early SRV-gank victories, and the bases are required to collect crystals, but it could have been totally possible to have games start with nothing but SRVs instead if your crystals were just stockpiled like in Age of Empires or something.)
Not to mention the act of getting a massive generation ship taken apart piecemeal and brought down to the surface of a planet would be a heavy undertaking that would far outweigh the benefits. It'd make more sense for a space-faring civilization to leave it in orbit where it can be used for spaceborne operations.
(Come to think of it, I wonder how it'd work if Master of Orion 2 had it where using a colony ship automatically creates a Star Base at any new colony...sure would prevent early-game rush tactics!)
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