Many of those "mobs" were led by ordained Catholic priests, such as Ferrand Martinez, who led a 1391 pogrom that killed 4,000 Jews. Forgive us if we don't distinguish between the "Church" and its ordained priests (who the Church did not excommunicate or even discipline for their slaughter).
And yes, the Inquisition may, technically, have had "ZERO jurisdiction" over non-Catholics. But, in the Inquisition's eye, Jews who accepted baptism on pain of death at the hands of an angry mob were Catholic. Children abducted from their families and then forcibly baptized were Catholic. Elderly women who lacked the ability to flee Spain in 1492 were Catholic. To the Church's or the Inquisition's eye, it didn't matter what the circumstances were of their "conversions."
By the way, this doesn't exactly seem to be true, if I read that article's summation of Pope Paul right. He said that people who were forced to convert could not be regarded as Christians.
Whether that was private opinion of his, or whether that was reflected in bulls/legislation of the time I don't know--I'm not a historian of the period. But it does seem at least that there was no automatic assumption that those forcibly baptized were full Christians.