My semi-educated guess is that it had to do with the fact that Bioko was the only one of those islands that had had a pre-existing indigenous population. One that at the time of that land transfer, still controlled the island’s interior. So it was undoubtedly the most disposable - the Portuguese had full control of the other islands and while Sao Tome had been a slave and sugar entrepot, Bioko was likely more of a headache than a revenue generator at that point.
Why Annobo is a harder question. Presumably it was just part of the bargaining and as was certainly less developed than Sao Tome and perhaps Principe and thus woth surrendering. In the case of Annobo, it is interesting that a Portuguese creole is still the most commonly spoken language and the inhabitants were apparently not happy about being to being transferred to Spain.