Alternate Skyrim removes the game intro, all signs of ongoing civilization, removes almost every non-animal, creature or undead, destroys almost all villages, destroys all cities, moves cities into the Tamriel Worldspace removing load doors and Navmeshes those changes so NPCs can use them seamlessly.
World Eater is a Draugr Apocalypse addon with Dragons and a mini Main Quest.
Alternate Skyrim and World Eater are likely incompatible with mods that make changes to existing Bethesda locations.
Mod added NPCs that never leave interior cells or instanced cities will also never appear without console commands.
Mods that will likely work without issue are gameplay, texture, mesh and sound mods.
Mods that add new locations away from existing Bethesda locations should also be fine.