Unfortunately open world requires compromises, mostly in the story dept. It's pretty much not possible to have an open world and an engaging, well constructive, tight narrative. They are diametrically opposed. Look at W3, (which handled the open world much better than most) it was a fantastic game, but compare the dlc "hearts of stone" to the main game. The dlc was stunning with an amazing antagonist.
Which you can't have in an open world game. Bethesda take some flak for their stories, but they know this very well. The big bad in an open world needs to be very much in the background with absolutely no sense of urgency attached to dealing with it.
You're vaguely aware that the dragon of doom is gonna eat the world, but first, you really need to pick some flowers, or chop some wood...
You can do both to some degree by offering a limited or staggered open world with areas that unlock as the main quest is completed. Baldur's Gate 1 did this - the entire southern half of the map is available to you from the beginning, but you're soft-locked out of doing too much exploring by your level/overall squishiness until after you complete the Nashkel mines. Then the game opens up in stages: Bandit camp (act 3), Cloakwood (act 4), and finally Baldur's Gate (act 5). It's both open enough to give the players lots to explore while also being fairly tightly controlled. PoE1 does something similar - the western bridge to Defiance Bay is cut off so as to encourage players to finish Gilded Vale/Raedric/Stronghold before moving on, after which the gorge leading to Twin Elms is flooded until the player completes Act 2.
The nature of Deadfire's setting makes it difficult to geographically block access to certain areas (they sort of do so with Ukaizo, but more than one 'impenetrable storm' would've felt cheesy), so I understand why the developers decided to leave it open. But imagine how much better the narrative flow would've been if a faction fleet had surrounded Hasongo and you had to complete quests/favors in order to get through, or if the shoals at Ashen Maw did gradual hull damage, forcing players to turn around after realizing that they needed to earn money for a stronger ship. That would have created both an in-game motivation to complete side content while also mitigating the urgency problem: it's no longer about whether you should prioritize going to Ashen Maw, but whether you are able to go there yet.
It's probably beyond the current capabilities of our talented modders, but I'd donate good money towards a mod that does something like this.