2 separate installs on one computer? without MO2

[lord satan]

Recently reinstalled SSE and this time I don't really want to mess up my main game by adding big, jiggly-titted bodies to every NPC including old women. I'd prefer to just have two separate instances of SSE. It's not as simple as just not loading certain ESPs since bodyslide necessitates overwriting body/clothing meshes, and it's not easy to undo that when you have so many mods installed. I would have assumed this would be easy, but when I install Skyrim on an external drive, it still forces INI & save paths to C:\Users\Me\Documents\My Games\Skyrim Special Edition

So if I install a second time to another directory, it will overwrite my settings.

If, instead of using the installer a second time, I just duplicate the entire Skyrim install folder and rename it something else, will it break anything? Is there something in the game that depends on specific, non-relative file paths?