I've just hit this rather frustrating issue myself. It isn't possible to independently configure naval & regular control schemes. Some actions appear to be intrinsically linked and must be bound to the same key (for example "sails up" and "jump"). That might make sense on a console with limited buttons but not on a PC. For example, "sails up" and "sails down" make far more sense being bound to W and S, respectively on a "WSAD" PC scheme (since they roughly correspond to "go faster" and "go slower"), but I don't want "Jump" and "Interact" re-bound like that, for obvious reasons.
Overall, this limits the usefulness of having two separate menus to configure the two sets of controls. The UX implies that the customisation has functionality which it does not. Since I happen to write software when I'm not playing games, here are some developer-friendly reproduction steps (since it seems that this was at issue previously).
- Playing Assassins Creed 3 remaster on PC, using the latest version published to Epic Store/UPlay as of 20th Oct 2020 (UK region if it matters)
- Enter the "customize controls" menu (not for boats/naval controls)
- Configure the "Interact" action to be bound to Right Mouse Button
- Leave the "customize controls" menu and enter the "customise boat controls" menu
- Configure the "Sails Down" action to be bound to the "S" key
- Leave "customize boat controls" and re-enter the "customize controls" (not boats) menu once again
Expected behaviour
In the customize controls menu, the "Interact" action should still be bound to the Right Mouse Button, as was performed in step 3.
Actual behaviour
The "Interact" action is now bound to the "S" key.
Also affects
I have also reproduced the same issue with the pair of "Jump" & "Sails up" actions. Changing one binding changes the other to the same key/mouse-button. The same problem also occurs in reverse. IE: If I make a configuration in the non-boat controls menu and take a look at the boat controls, the "linked" action has been changed.