There's always a heavy price to pay for having an open, non-linear game.
Deadfire does a lot to try and encourage you to explore, both by giving you quests in Neketaka that can only be done if you leave the city, and by tying a lot of triggers to advancing main quest, which again, requires you to leave the main city.
But if some people have a playstyle where they just methodically clear area after area, they will always just go back and continue cleaning, unless you force them not to. And that requires putting the game on rails. You can do it AoD style where the game is non-linear only within each act, but remaining content is blocked by plot-gates, or you can do it Wasteland 2 style with radiation zones, or you can do some various other shit.
But I think that with a seafaring game, it really had to be a no-compromise completely open, with no plot-gating, otherwise whatever the fuck is even a point of having a seafaring setting.
You make it so you reach max level in the city, and the challenges outside are not gated by level but encounter difficulty.
That will only fuck up the people who explore a lot from the start. There's no pleasing everybody.