Gaya and Bodh Gaya are about twelve kilometres apart and are constantly confused in general writing. They are different places with different religions, different pilgrim populations and different histories. Gaya is a Hindu city whose principal business is the rites for the dead. Bodh Gaya is the place where the Buddha is said to have reached enlightenment under the tree, and its Mahabodhi Temple is a Buddhist pilgrimage destination drawing visitors from across Asia. The atlas holds them as separate entities for that reason, and the confusion is worth naming rather than quietly avoiding, because a reader who conflates them will misread the pilgrimage figures for both.
Diana Eck's survey of Indian sacred geography also points to a genuine connection that is not the same as identity: the two sites sit in one landscape that Buddhist and Hindu traditions have each mapped, and the Buddhist tradition itself remembers Gaya, as a place the Buddha visited and preached at. Bodh Gaya's later history includes a long dispute over the management of the Mahabodhi Temple between Buddhist and Hindu parties, settled by a statutory committee under the Bodh Gaya Temple Act of 1949, which the atlas records under that site rather than this one.