

This is also why Skyrim.esm (the entire game of Skyrim with all its heightmaps, meshes, and textures) is loaded first.

If two mods change the same thing, such as the ebony sword recipe in Perrain's example, whichever mod is loaded last will overwrite the previous mods in the load order. Well load order is what allows us to change the vanilla (default/original) Skyrim. What does the order of the load have to do with the compatibility of the mods?
