It has to do with origins, purposes and ends.
At its worst, Ferdinand and Isabella required the Jews to either convert or leave their realm. Much of the justification of this was the idea that Jews living side-by-side with “conversos”, converts to Christianity, would lead the latter to stray from their new faith.
But to these modern philosophies, conversion or expulsion wasn’t enough. Jews had to be annihilated, as they believed in God, not the state, as supreme being. This is seen across the spectrum of philosophies. The state must destroy God to become the new god.
And this was not limited to just Jews.
I think we agree on many things, but I disagree on your conclusion of causes. Origins,purposes, and ends are justifications. What underlies those justifications is the true evil. Christianity, (mostly in the past) and islam today preach and teach hatred of Jews in particular. This is a rather Freudian in nature since the Jewish religion is the parent of both Christianity and Islam.
Judaism was not, obviously, a willing parent nor are the children legitimate in a marital analogy sense. This “family” although excessively disfunctional, is a family.
As a historical note, during the Inquistion many Jews were never given the option of leaving, many more forced to leave without family members and most had their property confiscated by the Crown and the Church. The Inquistion was as horrendus and as tragic as the Holocaust. The differences between the two is that the Spanish are simply less organized then the Germans.