There could be a penalty for multiple bases/planet, rather than a hard limit. Inefficiency (due to ships needing to share the space or whatever) sets in and at some point (as determined by the player) it isn't worth it any more. If makes more sense that a large, populous, densely industrialized world can support two bases than that a pair of newly minted and anemic colonies can each support one. Make each colony after the first cost 25% more than the last or something.
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