I don't think that Portugal would be incorporated into Castille. Juan I was not defending "his" claims to throne, but his wife's claims, Beatrice of Portugal. She was his second wife, and he already had two sons from Leonor of Aragon: Henry (who would become king of Castille) and Ferdinand (who became king of Aragon). IOTL he had a son with Beatrice, Miguel, who died in infancy. If the Castillians had won Aljubarrota, and Miguel had survived we wouldn't have a union of Castille and Portugal, but a dynastical change, with a Trastamara king in Portugal, Miguel I.
Even if their son do not survive as IOTL Juan's claim would be so weak that he could probably support one of Beatrice's uncles, John and Dinis, who were sons of Peter I of Portugal and Ines de Castro. They supported Juan I in his war against the Master of Aviz (the future John I of Portugal), and so an alliance is not that unlikely if Beatrice has no children.
So probably the Portuguese independence is granted. But one thing that would probably be changed are the naval explorations. The victory of the House of Aviz was the victory of the Portuguese Bourgeoisie against the most powerful nobles. If the Castillians win then the nobility would have more power and the merchants less, and the beggining of the explorations would be delayed, since the nobles were not interested in it.
Also, if Castille wins then the Anglo-Portuguese alliance is killed at its beggining. Portugal would probably follow a foreign relation that follows the Castillian one, until the next war between the Trastamaras happens.