Commenting on a historical period requires familiarity with the culture of that period in that place. Intentionally causing physical discomfort (to oneself) is a part of Catholic culture to this day. It is done, possibly on advice from a priest, to focus the mind rather than as punishment. Similarly, an inquisitor would make the suspected heretic suffer mild pain or discomfort because the inquisitor believes that would remind the suspect of the suffering of Jesus and the suffering of hell that awaits the suspect if he does not cooperate. It was done to motivate honesty and cooperation with the investigation. The Inquisition always reminded its cadre that torture that is so intense that it causes false confessions is not allowed. A typical instrument of torture was a metal stick with forked sharp ends; it was tied to the suspect's neck so that he has to keep his chin up to avoid pain.
Regarding specifically Spanish Jews, the Holy Inquisition concerned itself only with the dishonest Conversos, that is, precisely, Jewish converts to Christianity that secretly maintained their Jewish faith. By definition, the Spanish Inquisition was not interested in a Jew (or a follower of any other religion beside Catholic Christianity) who would declare himself such. Jews that kept their faith suffered expulsions and other injustices at the hand of the King's government, to be sure, but not at the hand of the Inquisition. Also, while explanations what the Kingdom of Spain did is not relevant for our discussion, Spain had just emerged from the prolonged war of reconquest with the Muslim and viewed Jews, rightly or wrongly, as colaborators with them.