The port upgrades are somewhat bugged.
As it turns out, RTW ports and their trade fleets are hardcoded. The first level (clearance) will give you one trade fleet. The second level (which says it is the first level to give trade fleets) will give you two trade fleets. And the third level will give you three trade fleets. Since some of the extensive port upgrades are level four or five of ports, they actually end up giving no benefits. Though, the small trade port upgrade ends up being level three for some towns, meaning it will give benefits.
For the most part, I just role-play extensive port upgrades. I'll just ignore the bug and build them for role-playing purposes even if I know they have no benefit.
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