The grant was conditional. Castile received the lands in order to bring their peoples to the faith, and Spanish law took that condition seriously enough to argue about it for a century. The requerimiento of 1513, a text read aloud to indigenous communities before hostilities, was drafted precisely to discharge it: it announced the papal donation, invited submission, and stated that any bloodshed that followed refusal would be the hearers' own fault. It was often read in Spanish, sometimes out of earshot of anyone, and it was ridiculed by Spanish observers at the time.
The condition also gave the critics their ground. Antonio de Montesinos preached against the encomienda in Hispaniola in 1511 on the footing that the crown's title was a trust and was being betrayed. Bartolome de las Casas built four decades of argument on the same premise, and Francisco de Vitoria at Salamanca went further, holding that the pope had no temporal jurisdiction over unbelievers and could not grant what he did not possess. Vitoria's lectures on the Indians, delivered in 1539, are one of the roots of the modern law of nations.
The atlas records both. Inter Caetera authorised a seizure and set a missionary condition on it, and the condition became the lever with which Spaniards attacked the seizure. Neither cancels the other.