This was done specifically to allow players to modify levels or create their own level packs. When Wolfenstein 3D took off, people were editing the base file, making it very hard to un-mod their games when they wanted to play vanilla. Id specifically separated the level stuff into WAD files to allow players to edit, create, or replace level stuff without effecting the actual base game, so they could always "un-mod" it. There's a good section about it in the book Masters of Doom.