- Does the main version affect\change anything in the game?
It doesn't affect the NPCs, only which eyes are available to you (the player) in the character creation menu; it also doesn't affect other eye mods you may be using, so any other new eyes will be available.
- Can I replace "X" with "Y"?
This mod comes with AO Clipping Fix meshes by Artsick (version 1.3, includes Invisibility Glitch Fix) + new meshes for new eyelashes based on same meshes.
You CAN replace all of the vanilla assets (meshes & textures) with whatever you want or not install them at all from this mod, it will not cause issues. I don't recommend it only because of visual consistency.
Read the ReadMe.txt inside the archive. You can download a 512p version for testing (replacer or not - the readme is the same), the archive weights only ~10 MB and the ReadMe.txt is the same.