No need to back up the game installation. But back up your user-directory with the save-files and discoveries, and so on.
The mods are set up to work with a pretty common modular design (not in games-development, just wtih programmers who know what they're doing). Where any includes or extra resources can be overridden or added when the game boots up. That's the... er... non-idiotic way to do it, because then you can have the game run perfectly fine and sort out any precedence problems during run-time. And you don't need to assign IDs by the billionth dozen globally for the entire project in order to avoid string conflicts (hello Aurora Engine folks at Bioware! How are you!).
So the mods are usually a packaged settings-file. That the game includes/parses when it runs, without replacing any files or other settings.
Like... there's maybe a block that says: "Sony Brown Halo FILter stuff".
It'll look like this
A file called global.ini might contain, among other things...
[Graphics settings]
(stuff)
[Sony Brown Halo Filter Stuff]
instagramfilter="Suicide Squad";
edge enhancement="NO DEPTH VISION HALP HALP I'M FALLING OFF MY CHAIR";
details="screw you PC FOLKS!":
It'd be packaged in a resource file of some sort, and are really just scripts that are parsed at run-time. That's when they're loaded, and all the other packages along with it.
And then other user-type graphics settings might be placed in a user.cfg somewhere, packaged in a similar way. It's also loaded at startup.
[Graphics settings]
[User settings]
resolution="teneightypee!"
details="PCMASTERRACE"
And these settings would typically be added to the [Graphics settings] tab, except for the ones that are already in the global.ini file, since this file would have precedence over the user.cfg. Or not, but just an example.
So to change that setting, you would add an include package for the global.ini file that has an edit. Which then supercedes the identical include, but does not screw over the additions in the user-cfg.
Optionally, the mods could add settings that may not have been used, or change values of existing settings in other include files that have similar precendence. I haven't looked at any of the NMS files, but that would be my best guess on how most of the mods are done.
So: even if the mods for NMS actually changes the game completely, and trigger some total apocalypse, or something like that. You can then just remove the include (the pkg-file), and it'll be back to normal again. It's really that simple.
Because HG haven't made an engine that, just taking another random Bioware example out of the air here, actually rewrites build files based on the includes in the toolkit. That was such a good idea. Absolutely fantastic. Is my override overridden by my own override from a different project that was overridden before by a patch from Bioware? I don't know - let's run the entire module through to find out! Etc.
No more of that.