Unity mod manager requieres you to set back your game files to original status before each update and offers a simple 1-click-solution for that. However, your point is valid as you have to rely on that restoration to work.

I have very little information regarding how exactly the engine alters the actual game files. So yeah, I guess it all comes down to trust in third-party solutions that - as far as I can tell - all seems to work reasonably well :)

I was looking into some of the mods, Unity Mod Manager and Pathfinder Mod Manager.

Most Unity mods hook into some Update() function which runs maybe 3 times a second and provide an alternative or additional code.
This makes the Unity Mod Manager code to load, but I am sure those are experts in the subject and do a good job not to slow down the game or break anything.
There is a different approach by the Pathfinder Mod Manager team, which loads their code by changing a setting in the machine.config for DotNet. This is much better and does not rely on any version of the games dll files. The files and code is altered in memory only (except for the DotNet settings file).

Then there are the mods, their code is loaded by the mod manager engine.

With the harmony library it hooks into the call of a function and just before it would be run, it runs alternative code from the mod to either alter the value passed to the function or replace it entirely.
All those go directly into the heart of the game and you don't know how the mods were coded or run. You need to trust and the game files they were based on change all the time at the moment, which makes error more and more likely or you always have to wait for the mod author to update before you can play again.

The Harmony thing is new though, before it was all extend or override of existing code. I need to read up on the subject myself.

Thanks for sharing this information on different modding approaches for the game. I will keep an eye on the less invasive methods.

Necroposting, lol.
There is a offline save editor utility(work in progress) which allows to reset MC to 0 and companions to its basics (1-3 lvl...) add some money and build points, edit item counts in inventory:
https://github.com/ericfitzgerald/KingmakerCharacterEditor
node, angular electron - Feel free to join!
Why not to use mod - it's a save editor, no changes to original games are made. And it's offline. Also, anyone can help updating the app.
p.s.: I'm not an author, just a commiter.