Here is the main part of the text: “We grant you [Kings of Spain and Portugal] by these present documents, with our Apostolic Authority, full and free permission to invade, search out, capture, and subjugate the Saracens and pagans and any other unbelievers and enemies of Christ wherever they may be, as well as their kingdoms, duchies, counties, principalities, and other property […] and to reduce their persons into perpetual servitude.”
The Catholic Church distinguishes between papal directives that do not arise from the Pope’s teaching office, and those which are not considered a part of the deposit of Faith, addressed to the entire Church vs. pronouncements that do so arise, and are so considered.
The Deposit of Faith is what Catholics are obliged to believe and follow.
I can’t defend or explain the papal permission to subjugate “the Saracens,” except to note that I do recall from my history that the Turkish Empire (Saracens) frequently raided, captured, and enslaved Christians throughout the Middle East, North Africa, the Balkans, and into the islands and coastal areas of Greece and Italy. The theory among the Turkish Empire, I believe was, that “infidels” in general (e.g. non-Muslims) had no rights at all, and were all considered to have the status of mere booty, to be made essentially cattle for the Empire.
The problem became so great, that a religious order was established whose main work was to raise funds and to ransom Christian captives of the Saracens. (The Mercedarians.)
It would seem that King Afonso wanted to make a vindictive response to the Saracen raids upon Christian communities. And the Pope approved his doing so.
This would be a one-off decision on the part of the Pope, and not applicable to the Church as a whole. Thus it is certainly defensible to view this bull as not in accord with the Gospel message of Christ.
That said, I wasn’t there; I don’t know the whole story.