In many ways, an Inquisition headquartered in Vodacce makes more sense than one headquartered in Castille. Consider: until the current Grand High Inquisitor took over, the Inquisition's primary concern was rooting out heretics and sorcerers. Can you think of any nation with fewer of either than Castille?
Besides, the Vodacce are known for executing runaway noblewomen, sometimes by fire. Many noblewomen are also strega. It doesn't take much for death by fire to go from a woman's punishment, to a witch's punishment, to a punishment for all kinds of sorcery and heresy.
Whereas the sorcerers of Castille were unaffected by fire.
This is presented as an alternate version of the Inquisition, to be used instead of the canonical standard. With some work, little else in canon is affected, except life for the strega in Vodacce.
A Brief History
The Inquisition was still started by the Third Prophet in Castille with the stated purpose of rooting out sorcerers in Theah.
But the Vodacce cardinals took an interest in this new institution. It had obvious power, and they wanted some recompense for the removal of the seat of Vaticine power from Numa to Vaticine City. They argued that, since the Inquisition had been so successful in removing sorcerers from Castille, it ought to now turn elsewhere. After all, what nation was more acutely threatened by the sin of sorcery than Vodacce? At this time, Montaigne sorcerers had to carefully hide their Porte, while Sorte strega could work fairly openly. But of course, a Castillian cardinal could never navigate Vodacce politics. The Grand High Inquisitor must be Vodacce. They buttressed their arguments with Vodacce staples of threats and bribery, and eventually the Inquisition came to Numa.
The Inquisition quickly became a player in Vodacce politics. The Grand High Inquisitor had power and influence on par with a Prince. The Princes resisted at first - the Inquisition was an unwanted new player in their Great Game. But the cardinals were the brothers and sons of the Princes and knew how to play, and it ended up being much less dreadful than anyone (except perhaps the strega) anticipated. The Princes use the threat of an Inquisitorial attack against their enemies' wives and daughters as a tool. The Inquisition uses its network of Vaticine churches and their excellent records to gather information and exert pressure on the Princes.
Vodacce's noblewomen were given one more reason to remain locked in their homes. Sorte is no longer openly practiced in Vodacce. But in their own homes, the women can sit and sew or spin, measuring out threads, snapping them, or making them. If their manipulations of the physical hide the metaphysical as well... who would know?
The Inquisition's history in Vodacce is as checkered as the history of any of the major families - sometimes it performed its assigned tasks conscientiously and without bias; more often, it played the Great Game with the rest.
The Inquisition did look outside of Vodacce as well, even if the efforts there did not receive quite the attention that home politics did. Just as the canonical Castillian Inquisition can have agents almost anywhere in Theah, so can its Vodacce counterpart. The Vodacce Inquisition is about as welcome in the different nations of Theah as its canonical counterpart.
The Inquisition is currently under the control of Cardinal Salvaza Rossi. In this round of the Great Game, she has elected to strike at Prince Caligari. After the death of the Hierophant, she suddenly declared that Syrneth artifacts were ungodly and corrupting, and that all research into them should cease.
(Thus we preserve the Inquisition as the foe of the Explorer's Society.)
Incidentally, the Inquisition (mostly Castillian members) were at the forefront of the attack on L'Empereur of Montaigne, after he openly declared himself a sorcerer and his nation a haven for sorcerers. However, in this alternate, they attacked at the command of the Castillian Heirophant. L'Empereur Leon still attacked Castille to "free it" from the Church's grip.
(Thus we preserve the proximate cause of the Montaigne-Castille war.)
Cardinal Verdugo of Castille is still the king's advisor and still head of the Inquisition in Castille. He still believes that the Fourth Prophet is coming, and that all seeking after of secular knowledge must stop. He has to cloak his actions under the Grand High Inquisitor's directive against Syrneth scholarship. When the dead scholars are found, after the fact, to have been investigating things entirely unrelated to the Syrneth, it's too late. There are murmurs of his removal (from the Inqusition, at least - one cardinal cannot unseat another), but Cardinal Rossi has yet to take action.
If Verdugo is less powerful and omnipresent in this version, he makes up for it by being more canny and by having better (if fewer) troops. The bulk of the Castillian Inquisition is tied up with fighting Montaigne sorcerers, but Verdugo maintains highly-trained units of fighting occult specialists. Fewer scientists are targeted by this Inquisition, but then, fewer are rescued as well.
(Thus preserving the Inquisition as the raison d'etre and foe of the Invisible College, at least temporarily.)
Fate Witches and the Inquisition
Sorte is the most subtle of Theah's sorceries. Anyone who is not a witch cannot tell for certain when a strega is manipulating the strands. But anyone who is a witch can.
The Church had long offered an option to cloister to Vodacce noblewomen who wanted to seek Theus through knowledge but whose blood was tainted with sorcery. They swore a holy oath to never again use their powers, were sequestered in a monastery, but were allowed to learn to read and given access to the Church's knowledge. Any found breaking their oath would be executed.
The Inquisition adopted this practice. Inquisitor strega are sworn to never touch the strands of Fate. However, they can still see the strands, and when another woman is manipulating them.
Perhaps obviously, they go hooded or masked, like the courtesans, at nearly all times. Their compatriots refer to them only as "Sister", never using a name that a witch might use to apply a curse. Still, many lead short or extremely unfortunate lives - the strega go out of their way to extract vengeance on these turncoats.
Grand High Inquisitor Cardinal Salvaza Rossi
I see all that I need to see.
The Rossi family are minor nobility under Prince Vestini. Salvaza Rossi was a pretty and charming little girl and her family hoped for a good marriage for her - until a fever at age ten left her blind. Now damaged goods, she was set aside and attention was lavished on her younger siblings instead.
At age twelve, her Sorte powers began to manifest. Inquisition or no Inquisition, this was still Vodacce, and a Fate Witch wife was still a good wife. She was trained.
For her part, Salvaza was glad to have some measure of sight back. She operates in a dark world of glowing threads that meet in knots that are people. Occassionally, a bright Arcana sheds some light in the void.
However, she held a grudge against her family for "abandoning" her after her fever. When her marriage was arranged at age sixteen, she fled to the nearest church and sobbed to the local priest to have pity on the "poor blind girl" who would undoubtedly be forced by her new husband to use her evil witchery on his behalf. She professed a desire to join the church instead. The priest, a good man, risked the anger of the Rossi family to assist her.
Salvaza actually had very little moral compunction about using her fairly formidable Sorte powers, but she would be damned if she'd use them to help anyone but Salvaza.
She softened somewhat in that stance as she rose up through the ranks of the church, gravitating to the Inquisition as a strega Inquisitor. Sorcery was a sin, and Sister Rossi did believe in the Vaticine faith. But... well, this was Vodacce. The ends justify the means.
She was made bishop by age thirty and, memorably, was thereafter accused of sorcery herself. She offered to undergo trial by ordeal to prove her innocence, even allowing her accuser to heat the metal rod. She grasped it and was unhurt. This minor miracle sealed her reputation as a holy woman chosen by Theus for great things. She made cardinal before she was forty.
She believes very much in her own reputation, to the point that she privately uses it to excuse her own workings on the fate strands. She has a dispensation from Theus to do his work. But sorcery in general - that's a dangerous sin and must be stamped out.
She does not like Syrneth artifacts but doesn't actually believe them to be instruments of heresy. However, declaring them to be makes it possible for her to bring her forces down on the Caligari family, the head of which is an obsessive collector of the things. And Beatrice Caligari, one of the most powerful Fate Witches now alive, is doing things to the strands that Cardinal Rossi can see the effects of clear in Numa. Whatever Beatrice is up to is exceedingly dangerous and must be stopped - at any cost.
The cardinal's "miracle" was the result of a Blood Science decoction thoughtfully provided by Alvara Arcinega (who likely arranged the trial). Based on Castillian blood, it prevented her from taking damage from the heated iron.
That credit has come due. Cardinal Rossi would like nothing better than to remove Esteban Verdugo from his post of High Inquisitor of Castille, but Arcinega is insisting that she keep him where he is. Verdugo is creating a climate of fear that is helping Arcinega's schemes, and he will expose Rossi's "miracle" if she does not comply.