The Article in Question
Defends the use of torture.
The Inquisition You Expect
Let's be clear about a few things. The Spanish Inquisition began as xenophobic, antisemitic arm of the secular government. The purpose was to identify and "identify" Spanish converts to Christianity from Judaism and their families who were said (or who were threatened or tortured into saying) to be practicing Judaism in secret.
From 1478 to 1525, the Inquisition probably executed around 2000 people and initiated around 15000 proceedings, which could and did involve torture, which could and did lead to corporal punishment and forced labor in galleys. People who "confessed" freely were often pressured into naming other people as part of the deal. Women imprisoned before and after trial might be raped by their jailers like Maria Deodata Fabri, otherwise sexually assaulted, or stripped naked for torture with multiple men looking on.
In the late 1560s, offices of the Inquisition in Valencia and Granada underwent a novel surge of xenophobia and Islamophobia and started going after communities of moriscos (forced converts from Islam to Christianity). Their targeting of these communities in light of Ottoman advances stoked even more public and government fear and helped drive the expulsion of the moriscos from their homeland.
In 1610, despite earlier attempts by Inquisition officials to reign in prosecutions of witchcraft cases and mitigate punishments, a major flare-up of witch hysteria in northern Spain mobilized inquisitors in Logrono. 31 people were accused of witchcraft; 6 were burned at the stake, 5 were sentenced to death but escaped justice (were "burned in effigy"), and 2 were exiled from their homes.
When Spain took over control of Portugal in 1580, the Portuguese Inquisition likewise became answerable to the Spanish government. In contrast to earlier lax policies, apparently it decided to prove its worth by initiating a new phase of trials and executions.
When these New Christian (yes, "New Christian" over a century later) communities fled wholesale into Spain, they escaped persecution...by paying off the Inquisition. This didn't last, there was a new wave of oppression, the king got into more financial trouble, the New Christians could suddenly buy their way out of persecution again.
Taken as a whole, the Spanish Inquisition was antisemitic and xenophobic. It was corrupt. It tortured people. It killed people in horrible ways based on rumor and confessions extracted during torture. It mixed Church and state with deadly results for its own citizens.
Now, let's talk about the Black Legend, confessionalization, and the Middle Ages.
The Black Legend
The article is correct in referring to a "propaganda campaign" emerging from Protestant writers in the later 16th century, as--yes--the Spanish Inquisition began to target Spanish Protestants as well. (Although never in the numbers that New Christians and moriscos were persecuted). The Black Legend is a racist and xenophobic story that makes Spain into the uniquely barbaric Other, and it draws a lot of its power from tales of "The Spanish Inquisition." It's the idea of a single institution, uniquely and inseparably Spanish, that had a stranglehold on the state and ideology for centuries.
That's a problem, because as you can already grok from my introduction, we can't really talk about The Policies Of The Spanish Inquisition. The patterns and intensity of inquisitorial proceedings varied enormously over time. Indeed, scholars unanimously now point to the early decades as the worst in terms of prosecutions and executions; I've highlighted the other major exceptionally awful periods as well. Additionally, there were mainstream Christian voices raised in protest at the beginning of the Inquisition and during its slow, unceremonious demise over the 18th century.
The Spanish Inquisition was very bad at times and in certain places (much like the article's vaunted comparison of witchcraft hysteria--another utterly horrific phenomenon whose reach and intensity is terrible to contemplate BUT also often overstated; historians estimate around 50,000 women and men were executed and another 50,000 acquitted or let off with lesser punishment). But it was also not bad at other times and in other places. It did not and does not reflect All Of Spain.
Confessionalization
So let's talk about some of the other times and places, or rather, parallel times/places of operation of the Inquisition.
There's a historiographical narrative for the Reformation/early modern era known as "confessionalization," with 'confession' being the label for the major Christian proto-denominations--Catholic, Lutheran, Calvinist/Reformed, Anglican. Confessionalization sees parallel processes of social discipline and secular centralization operating within and through the ideology and infrastructure of the different confessions.
In Spain, the Spanish Inquisition was an infrastructure linking Church and state (let's just roll with that term). It absolutely served as one of the bodies taking that steps that, to historians, constitute confessionalization.
After the mid-16C Council of Trent in particular, the Inquisition turned much of its gaze to wayward Christian practices--theological, ritual, or social. Sex/marriage crimes (bigamy, adultery, prostitution), blasphemy, believing the Virgin Mary was divine, not going to confession, superstition, witchcraft.
You'll notice those are a MAJOR variety of levels of "crime." This relates to what we define as separate phenomena, religious instruction/formation and social discipline, but were all part of the package. The goal is an orderly Christian society--whether that means Spanish Inquisition tribunals or Genevan consistory courts.
The Inquisition, also in parallel to the national churches in Protestant lands, served as a locus for state and Church to work out questions of authority. As a peninsula-wide institution answerable to the state, it participated in the secular government's consolidation of sovereignty over Spanish territory.
In these way, yes, the Spanish Inquisition participated in an ongoing, Europe-wide process that we see as leading to the modern world. Xenophobia, antisemitism, and Islamophobia are also part of the modern world, and also received fuel from the Inquisition.
The Middle Ages
Actually invented a lot of the "modern" judicial processes (or steps along the way) that the article credits the early modern Spanish Inquisition with.
Inquisitorial procedure (used in places that are not the US), confessions made under torture not counting, the idea of mitigating potential punishment by community restoration through penance, the defendant's right to name witnesses with a grudge against them--these are medieval and widespread. Also, the medieval inquisitions were by most accounts much sparser in their use of torture by physical pain.
Bottom Line
The Spanish Inquisition does not define Spain, but it helped make the country's modern shape in ways good, neutral, AND bad.