BUG and BAT? No - they need to be merged with the mods. Some of the mods lift stuff straight from BUG (because they love it!) and merge it themselves. Other mods have mod-mods that include BUG. BUG and BAT don't work with the mods that come with Civ4 ... ok, they might but don't expect it to be seamless. You could try it and, if you get errors (ie no interface), then you will need to exclude customassets when starting the Civ4 mod (see the option in the mod ini file).