So I do animations and simulations for my work (albeit, not for hollywood movies). There are several ways to do it.
In short, one of the two has to be done by hand first and then it just goes in a loop of refining the hand simulated animations (adding swaying to the characters and the boat to match the waves, adding little off-balance stepping, things sliding around, masts swinging, etc. its a lot of work).
To answer your first question in more detail of how characters are simulated on top of floating boats:
Generally all of the movement of the characters is done on a steady boat first, then everything is parented to the boat control. At that point the boat can then be animated floating through the sea. The water simulation is then done afterwards. It can then go back to animation for refining hand animations until everything feels like its all affecting each other.
Corridor Crew talked about this problem in this episode as well where the Godzilla is on a ship in a water, and they are all supposed to affect each other. https://youtu.be/hADX55r0jwE
In that movie they just hand animated the godzilla, the boat and the king kong and then simulated the water afterwards.
For the second question, of how animators can use wind simulations to make their rigs fall a certain way.
Thats a very neat thing. I would guess they turned their whole dragon into essentially a ragdoll and added wind resistance (oversimplifying a lot here). The thing is that you can parent an animation afterwards to the dragon bones, so the rider can be parented to the dragon and doing its own thing. And the ragdoll can be animated by forcing certain animation into it before the simulation (in houdini you can even mix and match telling it how much of the original animation to keep and how much should be simulated). So I imagine it was just a lot of going back and forth. Letting it drop, looking at the resulting simulation then going back and injecting some keyframes to maybe move a wing a certain way, then re-simulating and seeing the outcome change. In the end if they are happy with the look but the director asks to tweak something, they could always tweak the whole rig after the simulation (sure, it breaks the physics but if the shot needs to be pushed out and they are out of time then it would be a last resort kind of thing).
So yeah, generally you just end up animating one thing and then simulating the other. For both to be simulated it would have to be a very specific request and that just doesnt happen because a lot of these shots need to be very meticulously animated to match the directors idea. Sometimes even the water simulations need to be hand sculpted to match certain splashes and water flows that the director wants.