This is of course my simple opinion. Not an official doctrine or anything like that.
An initial argument. If "the devil" wanted to destroy the church, would he use a random sect from a remote country, or he would infiltrate the one true church?
The one who betrayed Jesus was inside his close circle. It was more "damaging" than a random guy out there. (Damaging but also God converted the "damage" into a tool for our redemption)
So for me, it is totally plausible that the beast would infiltrate and corrupt to some extent the Vatican. But I trust Jesus when he said "And the gates of hell shall not prevail against it." I should say that the Vatican is not the same as the Catholic church. But this "test", even very damaging and evil will be a tool for Jesus to prevail.
That being said Let us explore a bit the question or allegations.
The second proof... seven hills and seven mountains and there is only one city in the entire world that fits this description, The Vatican."
My initial comment was regarding this idea. If "the devil" wanted to usurp a "chair" he would target the "real chair". Imagine a historical battle where a usurper wanted to claim the crown of a country, would he target a random chair at a bar, or the one at the official residence? Even he is not the "chairman".
But Let's explore Rev. 17:9-10
"The seven heads are seven hills on which the woman sits. They are also seven kings..." In my opinion, trying to interpret Revelation as a textbook is a little pretentious. It says the hills "ARE ALSO" seven kings. I am not a theologian, but it is plausible that the hills are not a mass of land, but positions of power.
The Catholic Church also persecuted protestants... fled to America where they declared each individual had a right to freedom of worship.
I attribute this to human stupidity, not to any Christian doctrine. Your same argument could be used against protestants, for example regarding accusations of witchcraft.
There are different "interpretations of history". I am from a non-anglo country. Some historians of English-speaking countries, based on rivalry with the Spanish Crown, wrote history diminishing a lot of the Spanish institutions. This is part of "La leyenda negra". One example could be the Spanish Inquisition.
A historian wrote "Christopher F. Black, of the University of Glasgow, points out that the inquisitors were "more skeptical" of accusations of witchcraft than the judges of many Protestant and other Catholic states: "The Inquisitions, once fully established, consolidated the necessary "legal procedures in order to seek the salvation of souls and repentance rather than the corresponding punishments.
Is this a justification? No. Again I attribute this to human stupidity.
The third evidence... "And it was given authority over every tribe, people, language and nation".
Using this as an argument, I could think of the UN, money, or even Google or the internet.
The Catholic church is FAR to have authority over everyone. On the contrary, in a lot of cases, it is persecuted. I could use one of your own texts as proof "There are also thousands of websites online that make the same allegations". Not only websites, but governments, education, culture, etc.
It is crystal clear that priests use clothes made in Scarlet and Purple and there are golden cups all around during regular masses.
This idea hurts me. Let me explain why.
"She held a golden cup in her hand, filled with abominable things and the filth of her adulteries."
If "the devil" wants to do something sacrilegious would be this. The Why implies the reality that the "regular mass" that the cup holds, is the true blood of Jesus.
For me, it is clear, that Jesus asks his disciples to do this Luke 22:19 "This is my body given for you; do this in remembrance of me". One of the maximum offenses would be mocking the most sacred of things.
For me, the beast mocking this, is proof of the reality of the mass in the first place.
It hurts me... The idea that people stepped on the blood of Jesus on the Calvary. There are many sacrilegious acts regarding the Eucharist.
I know protestants do not consider that the real blood or body. Just be respectful, not for the catholic, but for the remote, just the remote possibility: Mathew 27:54 "Truly this was the Son of God" And one day you don't say: "Truly this was his blood and body".
the Pope transferred the day of worship from Saturday to Sunday
I could argue was not the Pope. I would argue that "Dominus" day, Domingo in Spanish, was the day the Lord defeated deth. Dominusday is the day we should celebrate.
The old alliance was with the blood of the lambs in the door's lintel. The New Alliance is with the blood of THE LAMB, Jesus. As Paul say: in 1 Corinthians 15:14 "And if Christ has not been raised, our preaching is useless and so is your faith"
Our faith is not based on Jesus' Death but on his resurrection. This is DominusDay.
In short. Even if the scriptures refer to the Vatican, We know that is a test. The church will be put to a test, the same way Israeli people were.
These are just some opinions of a random dude. God bless you.