Example with RFWC:

1. Enable Mod
2. Launch game
3. Change keybinding for "Drop/Weigh Anchor" from "Z" (default) to ";"
4. Apply changes
5. Quit game
6. day_preset_Users.xml shows:

<input name="UARFWCAnchor">
    <btn name="kSemicolon" />
</input>

7. Launch game
8. Check keybinding - displaying ";" as expected
9. Remove keybinding by clicking the "x"
10. Apply changes
11. Quit game
12. day_preset_Users.xml shows:

<input name="UARFWCAnchor" />

13. Launch game
14. Check keybinding - displaying "Z"
15. Quit game, day_preset_Users.xml has identical content as before
16. Launch game, change keybinding for "Fast Throttle Change" to ";", apply and quit
17. day_preset_Users.xml shows:

<input name="UARFWCFastChange">
    <btn name="kSemicolon" />
</input>
<input name="UARFWCAnchor" />

18. Launch game, check bindings, bindings showing as ";" and "Z" respectively.

I tested this process for the other mods with identical results - unbound mod keybinds are bound to default when loaded, even though day_preset_Users.xml shows as unbound.
Vanilla keybinds work as expected and remain unbound on game relaunch.