I think the author try to imposing his "wish" on how the event should be, by creating the conspiracy between Islam and Roman catholic. First of all there are different interpretation between Islam and Catholics or Christian in general on how they see certain event, the easiest is regarding Jesus, as the Catholics believe Jesus is God himself manifest in the form of human being, while we muslim believe that Jesus (pbuh) is part of the chain of the prophet, just like Moses (pbuh), Solomon (pbuh) or Muhammad (pbuh). Also other event like what happen to the peoples of Noah (pbuh)? or whom is the one who been sacrifice by Abraham (pbuh)? And many other.
So we have very separated view regarding how we understand the history, how we understand the Oneness (not unity or league of God) of God (monotheism or Tauhid), how we understand the divinity of Jesus which in Christianity there almost no dispute that Jesus is Godly divine, but the dispute between the Monophysite, Coptic, Orthodox, Catholic, Protestant (etc) is regarding how Godly divine Jesus is, while the Muslim in oppositely state that Jesus is nothing but a creation, a man, a mortal, a prophet that not different than other prophet.
To say that Islam is a part of Catholic sect, at least they must have share the fundament and crucial things which is the view on Jesus divinity. But this attempt on seeing that Islam is nothing but a copy of Christianity is not started by the Protestant but way way before that, so what protestant state here is not at all a new things, it just a re-manufacture of what the early Christian (before protestant) want peoples to believe on what Islam is way before they (protestant) come to existent.
And to state Waraqa Ibn Nawfal is a catholic it is a one way that we can see how the author want to fit his wish into his interpretation. He is not a catholic, most probably by the way the classic narration narrate him he can be Arian (who may be run from the persecution) but that also from my own assumption that have no prove and even contradict to how his view regarding the divinity of Jesus. According to the Quran, hadith, the record of the living sunnah also classic muslim historian (you can easily refer to the testimony of Salam Al Farisi) there were minority sect of Christian at that time that see Jesus as the prophet of God not as the manifestation of God.
While Khadijah in all recorded history was an idol worshipper before Islam, not Christian, so all this claim are impose to be fit with the wishful thinking of the author.
I can claim back, that both the Iconoclast and Protestant appearance are the effect of the influence of Islam toward Christianity, I see this claim far more logical eventhough I never bother or discuss about this, but in comparison I think that more valid than the claim in your's link. And what do you think about that Masada?