I see what you mean now. Hard and Realistic are just presets for how many boxes will be activated, anything else being 'Custom'. What counts is the overall % value for difficulty.
To know if there are hidden values, open the *.cfg file in your savegame folder and go look for the values. If some values are there but not present in the game options, then they were hidden. None of them are hidden AFAIK.
In TWoS you can only get 99% by putting everything to highest difficulty. For 100% you must play at Real Navigation + something else I don't remember.
And then, of course there are other settings through the mod: It's called OFEV, Options File Editor Viewer with a ton of options, albeit no difficulty options AFAIK.
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