For sure, the boundary is a grey zone. We can disagree on where exactly it is. But just because we disagree on shades of grey doesn't mean that black and white are the same thing.
I, personally, would just about consider EU4 alt-history rather than only history-flavoured.
This blog goes into the accuracy of its systems in great detail. The fact that it respects time and space matters a lot. It also models the interactions between things that are below the players immediate control to a substantial degree. For example, the complex network of trade flowing from node to node feels like it has a life of its own, and the player can interact to nudge it, but
never very rarely control it. That's not to say that EU4 is a perfect emulation where everything that matters in real history is modelled one-to-one in the game (even attempting that would be insane IMO). But I think it does a decent enough job of abstracting those away to create a simulation of the higher level consequences to be called an alt-history simulator. An imperfect one, with far too much player autocracy, but the same things that weaken it as a history simulator strength it as a game.
So while Civilization is on the same spectrum, it's much further to the extreme of history-flavoured rather than alt-history. I'd say maybe the Total War series falls somewhere between Civ and EU4?
Actually, while EU2 was very much an example of "alt-history" (especially after the excellent work done by the Alternate Grand Campaign/Event Exchange Project mod!), I think EU4 tends to be much more unmoored from history, to the point where I don't think of it as alt-history anymore, but, rather, play-history.
It's interesting that I was thinking earlier today about just how to think about games and their "historicity". EU, and EU2 were interesting in that the events in the game forced the player to re-live the actual history of the country they were playing. It meant that major historical events (like the end of the Hundred Years War) were impossible to avoid, regardless of choices one made that, in reality, would have prevented those events from occurring. That meant that a player of EU2 ended up VERY immersed in their country's history (I used to do extensive research into the history of a country I played, especially in MP, and REALLY especially if I was writing some sort of ongoing AAR. That's been much less true with EU4, where historicity can be thrown out the window in most cases. It's like playing with the building blocks of history; call it LEGO history.
By comparison,
Civilization and its progeny have never been about being historical. I mean, seriously, a game which allows you to start in 4000 BC as the Americans? Which from its initial iteration involved no guarantee that traditional historical rivals would even be able to meet (in
Civ, the Germans or the French can play, but not both!)? A game that had you researching only one technological advance at a time? You can learn to sail, or you can learn to make bronze spears, but you can't be doing both at the same time? A game that allowed historical AI leaders to undertake actions that they would never have countenanced in real life (and I don't just mean Mr. Nuking Gandhi!). The game wasn't historical at all! What it DID have was a whole bunch of what we might call the Name, Image, and Likeness of History. Romans, English, Mongols, etc. Accurate city names. The Ancient (and modern!) Wonders of the World. Military units from antiquity, and from modern times. For anyone with a bent to studying things historical, the game has always been a wonderful toy. But we didn't get deeply into it because of its "historicity", since it had very little.*
To use the metaphor from the OP: I think
Civ isn't even history flavored; I think it's simply
Iron Chef, where you have to produce a completed meal using standard historical ingredients. Yeah, maybe we've stretched that metaphor a bit thin, but it seems pretty apt, especially when one thinks about playing the game in MP.
A different analogy is
Star Trek. The
Next Generation was somewhat flavored like the original; it was really Gene Roddenberry's attempt to make the show he intended in the first place, and couldn't because the network wanted more "Action!" (usually involving getting Kirk to tear his shirt and kiss someone). But modern Trek shows aren't really Star Trek flavored, even; they are, in my opinion, just shows that use the original names and concepts, but re-work them to have a different kind of fun. That's Civ in a nutshell.
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* I will note that I do think the two things that gave it some historical flavor were the tech tree, which, while an artificial limitation on technological advance, did attempt to tie things together in much the way that James Burke showed us in
Connections; and the whole inter-relationship of food, hammers, and gold. That mini-lesson in social economics was especially intriguing; one of the most fun parts of taking on a new iteration of
Civ is learning just how they have mucked around with that!