By the time the first Europeans settled in the New World, English, French, and Spanish heads of state had all established degrees of independence from Rome. However, the papal bulls that formed the basis of the
Doctrine of Discovery remained a convenient justification for the taking of Indigenous lands that continues to this day.
Probably born somewhere within 10 years or so of Columbus' discovery of America, Francisco de Vitoria proposed a "kinder, gentler" Doctrine of Discovery. In his Relectio Des Indis, Francisco de Vitoria argued Spain's right to travel among the Indians and trade with them based both on Divine Law and what he termed the "Law of Nations." Neither of which, of course, Aboriginal peoples had been party to.
In a nutshell, Francisco de Vitoria posited that it would be downright unneighborly of the Indians to throw the Spanish out or not trade with them. However, unlike the The Bull Romanus Pontifex and the Bull Inter Caetera according to which the end justified the means, de Vitoria argued that reason and persuasion should be the first recourse. However, if "...after this recourse to reason, the barbarians decline to agree and propose to use force, the Spaniards can defend themselves and do all that consists with their own safety, it being lawful to repel force by force." It is also noted that Indians, being "dull and stupid" might misunderstand the good intentions of the Spaniards and make war on them. In that case, the Spaniards could defend themselves but not "slay them or despoil them of their goods or seize their cities." However, if persuasion or limited war still didn't suffice then all bets are off. Cities could be seized and subjugation was acceptable.
By the time the Doctrine of Discovery was cited in the Marshall Trilogy, it no longer espoused torture and slavery, and, under Francisco de Vitoria, had become as much a political as legal doctrine. As such, it served a great convenience when nations needed a rationale for stealing indigenous lands. US Supreme Court Justice Ruth Bader Ginsberg--the liberal judge--cited the Doctrine of Discovery in a recent judgment denying trust status to an Oneida land purchase that lay clearly within the historic boundaries of its nation.
The Doctrine of Discovery applies even today.