That's why I asked for the installer. Let me explain how these files work first. The game uses .rim files for each level to store their data. These files are basically containers including all the necessary files that make up a level. Now, you could just modify the files inside that .rim file but that would be irreversible without reinstalling the game, so instead you can copy a file from the .rim to your Override directory and modify it there. This file in the override will now be used instead of the original one from the .rim but can easily be uninstalled by simply deleting it. The game will then use the original one again.
But there can be several reasons why you don't want a certain file in your override and that's where the .mod files come into play. .mod files are basically copies of the .rim files in that they also store all the necessary files but if both a .mod and a .rim file exists for the same level, the .mod file will be used. So similar to a file in the override, you can safely delete the .mod and the game will use the original again. This makes compability a problem however since there are many files in each .mod and most mods only edit some of them. If they'd just provide the .mod file you could only install one of them, that's why TSLPatcher is so useful.
TSLPatcher will edit the files already existing in a .mod file instead of replacing the entire .mod. But since the .mod files do not exist by default, mod authors ship a .mod file that includes all the unedited level files with their mod. TSLPatcher will then install this .mod and make all the changes inside unless the .mod already existed. Then it will just edit the one already there. And this is exactly the reason for your warnings.
Don't worry about them, they won't cause any troubles, but if you copy the .mod files from K1R into your mod folder you will revert all changes made to them by both NPCOverhaul and K1R since what you're copying is the unmodified version.
Sorry for the long text, but I hope that this explanation can make things clearer for you when it comes to installing mods.