Okay.......does TNR work with the Natural Faces? or does it use the textures?
I think you have your mod parts mixed up. TNR is only a set of plugins. It changes the face settings data for individual NPCs. That has nothing to do with what textures the head mesh loads from among your files. You can swap textures in and out as you please. The data is not stored in the game, and the only awareness a plugin may have of a textures is that there is a texture XX at Textures\Clothes\LowerClass\ or something. As long as the file is found, things are all good. That is why I say that texture replacer can only really break the game by requiring too much of your GPU. They do not affect how the game
works, how various things interact in the game; They only affect how things look. The same goes for sound files; They only affect what you hear, not how anything works. The game will run fine without them, even textures, although the solid violet meshes without their textures may be a bit disturbing to play with. Mesh replacers also work like this, but putting in the wrong meshes can be slightly more problematic.
Also, to the thread (title) question, IFT will only affect the races for which installed. If your PC is one of those races (the Vanilla races) then, yes, the PC will be affected. Again, the game is told to load the face textures associated with that race. If IFT's textures are there (and BSA redirection is implemented) the game will load them. If you put in Natural Faces' textures, the game will load those. You can put any texture file there, and the game will load it if it can.
Edit: wording