So, taking our chair01.nif example, and you have SMIM, Better Furniture (sample name), Improved Furniture (sample name), and Immersive Furniture (sample name), then you would have to pick which one will overwrite the vanilla file and be named chair01.nif. If you want to use multiple mods that do the same thing, you will have to open them and ensure the assets all have different names, and their loose files will have to be renamed to match how you renamed them in the mod.
It doesn't go by which one you like more, or which one is objectively 'better', or any other criteria than the name. If multiple mods have that same filename for ANY mesh - chair01.nif, for example, whether one mod uses that name for the vanilla chair01.nif or not - then that's all the game looks for. The game looks for a specific filename for a specific mesh.
Are these loose files? If so, by what logic are you expecting the filenames to be different?
