Should a city be able to ban/allow pirate ships from docking?

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There is however one, simple, inescapable fact. It dropped certificates. Not materials.

If they wanted weight, they'd give you materials. You drop certificates on death, so it's not to protect from that. It can have only one purpose: To make it so that looting a caravan isn't entirely useless because a person can't carry more than a tiny fraction of the loot away after. Caravans exist to carry far more than a player can.

Certs are the way that players can loot a caravan at all.

Having to take them back to the node of origin only reinforces this interpretation. The only purpose such a rule can have is to prevent players from exploiting and bypassing the system by carrying materials to their destination in larger quantities than a normal inventory could. Otherwise it would just be normal gameplay.

Competent developers don't add pointless systems. The only valid assumption is that you can carry more "Iron Ore Certificates" than you can carry Iron Ore.