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foo_: Few if any games ever use windows text mode for input. It's too slow and too difficult to cater for all the differences. Usually raw input events (or even the deprecated DirectInput) are used, pretty similar to the USB HID events.
So any effective key mapping needs to take place early in the input processing chain. Forget about the user panel.
Software for mapping (like the oft-mentioned AutoHotKey), mapping at driver level, and on the device itself will work.
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mmarci: The problem here is that the game overrides these for an odd reason, in a very unusual way. Every key works except for the mouse buttons. What can be the explanation for it works on the main menu screen once you start the game, but as soon as you go to any of the sub-menus, it reverts back to default? Why would it assign LButton to both buttons in-game, and RButton to both buttons in the in-game menu?
About the OS and environment, I've got some knowledge,
but what the game does internally and why, I can only guess - and its input handling looks inconsistent to me. As if somebody had a proper plan, and then somebody else ignored that in parts.

Sorry, I think the only people who really can answer your specific question are CDPR.
There is of course the input.settings file (open in notepad) in the User\Documents\The Witcher 3\ folder but it only really changes the actions within the game and not the menu stuff.
Do not download Autohotkey from http://www.autohotkey.com/ it is a quite outdated version you will find there.
Download from http://ahkscript.org/ instead.

The following is quoted from ahkscript.org:

Why ahkscript.org?
AHKScript.org is a new community consisting of the active AutoHotkey developer(s) as well as other enthusiasts. Unfortunately, the old autohotkey.com domain is not under the control of the developers and it continues to promote an outdated version of the software. New users are encouraged to migrate and participate at this new site.

end of quote

If in doubt of the validity of this claim. Go to Wikipedia's description of AutoHotkey and follow the download link shown there.
I believe that a bad/fraudulent link in wikipedia wold be removed rather quickly.

==============

And now something different.

When using autohotkey to remap keys you wold want to limit the remapping to only work within a specific game.
you can accomplish this by using the following code block. (using the wither 3 as example)

------
#IfWinActive, ahk_exe witcher3.exe
; Put script for the game here. something like
q::x
x::q
return

Please know that the ahk_exe clause used above do not work on the outdated version of AutoHotkey you get at http://www.autohotkey.com/ if using that version you have to use the following code-block instead (for witcher 3)

;The Witcher 3
#IfWinActive, ahk_class W2ViewportClass
; Put script for the game here. something like
q::x
x::q
return

/regards
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Agrilla: Do not download Autohotkey from http://www.autohotkey.com/ it is a quite outdated version you will find there.
Download from http://ahkscript.org/ instead.

...

When using autohotkey to remap keys you wold want to limit the remapping to only work within a specific game.
you can accomplish this by using the following code block. (using the wither 3 as example)

------
#IfWinActive, ahk_exe witcher3.exe
; Put script for the game here. something like
q::x
x::q
return

Please know that the ahk_exe clause used above do not work on the outdated version of AutoHotkey you get at http://www.autohotkey.com/ if using that version you have to use the following code-block instead (for witcher 3)

;The Witcher 3
#IfWinActive, ahk_class W2ViewportClass
; Put script for the game here. something like
q::x
x::q
return

/regards
Thanks very much Agrilla, I updated the links and doing the same for my posts as well. If you have a solution to swap mouse keys that work in-game, please share.