It's never made sense to me to call what's obviously just a docking platform with some cargo cranes a "shipyard". On the other hand, when we can completely rebuild our own ship from the ground up, changing the hull shape and everything (the Radar upgrades), it makes no sense for the only source of cargo ships to be trade. And yes, I'm being specific to new cargo ships, not the few damaged ones that we have to repair in the wild instead of towing home for that.
That, and cargo ships seem... shockingly cheap, actually, when acquired through trade. Or maybe that's just my high-economy patient playstyle, but they do seem to be significantly cheaper than our core ship, despite being... bigger? That and there's 4 sizes of cargo ship, and they just magically change size...
Enter, the Drydock. Manufacture cargo ships for use as trade goods (now we're selling cargo ships, not just buying them), modify them to change module layouts (the magic module changing with depot setup makes no sense, when trains and Mega vehicles can't do that), module counts (making 5-module ships possible, for those trades where we currently have to leave 1 bay completely empty because there's no way to actually use it), fuel types (rather than sending them to the open ocean to modify the engine, I mean who does that?), engine upgrades (because no two engines are quite the same, and changing the size of a cargo ship doesn't magically change the size of its engine to match), hull upgrades (maybe the sea is rougher further out, requiring a reinforced hull to reach those settlements or world mines), possibly even take contracts to modify cargo ships belonging to other settlements (selling a service rather than a product), and so on. This could even be where we send our main ship for the hull-modifying upgrades like Radar, as it makes no sense to change the shape of the hull while it is floating.
You could even, at least in theory, use the Drydock to manufacture a second Main Ship for accelerated World Map exploration (probably a significant technical change to support multiple exploration ships), or perhaps to enable fleet combat against even deadlier pirate encounters. This would also make it possible to implement Main Ship sinking, as it could then be replaced. Or even Cargo Ship sinking, though I'm not sure how that threat would be implemented so as not to seem unfair, which would create an ongoing use for the Drydock beyond the production of trade goods.
On the topic of the World Map, I'd like to have a larger World Map with more places to explore. At the moment, it feels like an early minigame that just goes away, causing the Main Ship to become a useless lump of metal parked next to my island after a while- especially once all the World Mines are depleted, and there becomes absolutely nothing that it even can do, aside from wasting fuel floating in circles.