The Near East is a scholar's unit rather than anyone's homeland, and the atlas keeps it because a great deal of religious material only makes sense at that scale.
Take the flood. A version survives in Sumerian, another in the Akkadian Atrahasis, another inside the Gilgamesh epic, and another in Genesis, and they share a structure that includes a warned survivor, a boat, animals, a landing on a mountain and a sacrifice afterwards that the gods or God smell. Nobody reading only one of them would guess at the relationship. The same is true of the treaty form: the covenant language of Deuteronomy, with its historical preamble, stipulations, witnesses, blessings and curses, follows the shape of Hittite and later Assyrian vassal treaties closely enough that the borrowing is not seriously disputed.
Temple architecture and personnel move the same way. A tripartite plan with an increasingly restricted inner room, a resident deity fed and clothed daily, a landed estate supporting the establishment and a priesthood organised in shifts recurs from Sumer to Ugarit to Jerusalem with local variation.
The atlas holds Mesopotamia, the Levant, Anatolia, Egypt, Persia and Arabia as separate regions because most material belongs to one of them. This entry exists for what belongs to the pattern rather than to any single place, and for the comparative arguments that pattern generates.