The basic question here is not some “Doctrine of Discovery.” It’s the right of nations to fight wars, to conquer other countries, and to rule by right of conquest. (Subject to just war doctrine and international law.)
So this has nothing to do with the race of the people involved. It had something to do with whether the people involved were pagan, but that’s about it.
The Bible did not condemn the Roman Empire for its conquests, or the Persian Empire either. We’re told that King Darius was given his conquests by God.
And here’s Second Maccabees on the Roman Republic:
"Now Judah [Maccabee] heard of the fame of the Romans, that they are powerful and strong, and willingly agree to all things that are requested of them: and that whosoever have come to them, they have made amity with them, and that they are mighty in power.
"And they heard of their battles, and their noble acts, which they had done in Galatia, how they conquered them, and brought them under tribute. And how they had done great things in the land of Spain, and that they had brought under their power the mines of silver and of gold that are there, and had gotten possession of all the place by their counsel and patience. And had conquered places that were very far off from them, and kings that came against them from the ends of the earth, and had overthrown them with great slaughter: and the rest pay them tribute every year. And that they had defeated in battle Philip, and Perses the king of the Ceteans, and the rest that had borne arms against them, and had conquered them. And how Antiochus the great king of Asia, who went to fight against them, having a hundred and twenty elephants, with horsemen, and chariots, and a very great army, was routed by them. And how they took him alive, and appointed to him, that both he and they that should reign after him, should pay a great tribute, and that he should give hostages, and that which was agreed upon. And the country of the Indians, and of the Medes, and of the Lydians, some of their best provinces: and those which they had taken from them they gave to king Eumenes. And that they who were in Greece had a mind to go and to destroy them: and they had knowledge thereof. And they sent a general against them, and fought with them, and many of them were slain, and they carried away their wives and their children captives, and spoiled them, and took possession of their land, and threw down their walls, and brought them to be their servants unto this day.
“And the other kingdoms, and islands, that at any time had resisted them, they had destroyed and brought under their power. But with their friends, and such as relied upon them, they kept amity, and had conquered kingdoms that were near, and that were far off: for all that heard their name, were afraid of them. That whom they had a mind to help to a kingdom, those reigned: and whom they would, they deposed from a kingdom: and they were greatly exalted.”
Now, you can say various things about the accuracy of what Judah Maccabee heard. But the point is that he didn’t think badly of the Romans because they did a lot of conquering of their fellow Caucasians. He didn’t sit there going, “Oh, if only the Romans were conquering unknown peoples with funny skin colors, because that would be so much more just.” Oh, heck no.
In the ancient and medieval world, and for most of the lives of the Spanish and Portuguese before they got ships heading for America or Africa, war was something you waged against your neighbors and cousins who looked just like you; and conquest was when you got lucky enough to make a war stick.
Now, sadly, warring against your neighbors and against the Moorish kingdoms (who, thanks to intermarriage with captives, were a very blond and blue-eyed bunch) and the Basques – that was not exactly the way to teach people to war nicely and treat captives kindly. Civil war and treachery among cousins gets very nasty very fast.
The reason the Portuguese wanted the African slave trade was because the Muslims had been making money with it for more than a thousand years (except with Muslims it was also the “white people of the Mediterranean and Atlantic basin” slave trade, and it continued into the 1800’s, including such illustrious victims as St. Vincent de Paul; their black slave trade continues to this day in places like Sudan, and King Saud brought one of his favorite black slaves to the League of Nations talks). The Spanish tried to do the same thing with Native Americans, but it didn’t work so well. Obviously both the Spanish and Portuguese should have known better; but unlike most of the rest of Europe, they regarded slavery as something you commonly did to people who lost wars.
But the kind of stuff that the Spanish and Portuguese got up to, against indigenous natives of the New World, was exactly the kind of thing that people also did in the Old World wherever the Church didn’t have much sway – except that in the Old World things were sometimes worse. You do realize that 17th and 18th century England openly condemned Scottish, Irish, and English political prisoners to slavery in Jamaica, right? That wasn’t about race or even religion (although it happened to Catholics more often); it was about the power of the state. Similarly, when Romanian lords forcibly settled Romany people and turned them into serfs or outright slaves, that wasn’t about evangelization or anything else but grabbiness.
Medieval times were usually marked by a gradual expansion of rights for common people. After the Reformation, there’s an expansion of grabbiness and authoritarianism, by everyone who found it convenient to reject natural law. The Church generally tried to rein in the madness, but didn’t always succeed.