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It's a different design paradigm than mass manufacturing. Huge refineries and assembly lines are setup because they build large quantities cheaply. Not because this large apparatus is inherently necessary for construction.

Think about it a different way. Imagine you had a robot arm with attachments for every type of tool. Grippers, welders, drills, nut drivers, hammers, etc... Couldn't this single arm build anything given the proper schematic and enough time? To further reduce complexity, you could add design constraints to your 'replicating spaceship' so that only a subset of tools would be required. Finally consider what tools could build the other tools. At some point you approach a minimum amount of gear needed.

Consider that the minimum amount of gear needed could potentially be under 200lbs in weight and under two meters in height.

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