Despite Castlevania being a world full of supernatural enemies, it is still a world very similar to our own. Fans notice these little tid-bits and can't help but point them out. This is why IGA should have done just a bit more research regardless if the CV universe isn't exactly like our own.
The opening story of LoI states that the church was more interested in fighting heathens, not monsters, which was why Leon left the order. So I do have doubts about the Crusades starting several years earlier because of the supernatural. The opening story dictates otherwise. The Crusades were all about securing the holy land for the Roman Catholic church and this view remained unchanged even in LoI.
I mean, preaching to the converted there.
But my point is that, in a greater scope, the point of divergence in the two histories is likely centuries earlier, with the existence of vampires and monsters having affected history in lots of "little" ways, like the flap-flap-flap of a butterfly's wings. After all, the Church is clearly AWARE of these monsters (they are just not the priority) and is shown later on to have at least one internal division dedicated specifically to fighting them and bankrolling several others, which the Church... verifiable doesn't have and didn't really do.
Who knows? A vampire's manipulations might trigger a war where none happened in our history, and I wouldn't rule out Death deliberately TRIGGERING the Crusades a few years early just for funsies. In fact, depending on how long-term a planner you want to say Death or Mathias is, he might have triggered the Crusades in the first place simply because the Crusades being active in 1094 is a big part of WHY Leon was in Eternal Night to begin with, making Mathias' plan (at least as it happens in game) possible.
After all, Mathias' plan has all the hallmarks of a Batman Gambit, which means everyone the plan accounts for has to behave exactly as the planner anticipates they will, which means NOTHING can be left to chance as the slightest deviation has a strong potential to ruin the whole strategem, which combined with Mathias being called a "genius tactician" reinforces that claim -- he did his homework THAT MUCH. That being said, he's also something of a Xanatos-type, which means he probably had back up plans on top of backup plans in case he catastrophically misjudged Walter, Leon, or Rinaldo, however unlikely that would be.
Death shown to be a similar planner in his few appearances with spoken dialog, so I don't have an ounce of trouble believing he was involved in Early Crusades, regardless of what the canon actually says; it's just something that would be very in-character for him to do anyway.
But all of that is to say this: the existence of fairy tale monsters has INCALCULABLE potential effects on history, and Castlevania's history's parallel course to our own nevertheless DID branch off, and my assertion is that it (very plausibly) branched off WELL BEFORE 1094, and even before Leon and Mathias' lifetimes. And while this doesn't excuse ineffective homework on the part of the dev team, it does at least make room to explain why things ARE that way in that the hypothesis fits the evidence at hand as presented in the games, and even a contradiction with another canon account doesn't really meaningfully affect anything.