I myself think it's apart of a couple of tropes coming together into a toxic mess that tends to create that particular cocktail.
One is ''under or nazi dog'' people tend to admire underdogs and rebels, indeed just add rebel trope will increase a books popularity by a bit. Of course to prevent the audience from rooting for the potential rebel one must twist their placing by making the country their are trying gain freedom from the real rebels if that makes sense. By that they turn the rebel country often into a seeming reincarnation of Nazi's or a clone not because they are just evil rather they do it because that way they claim a tradition of victory and oppression that was very successful and in turn the country fighting them can claim to be in turn the tradition of righteous victims of oppression fighting them and or inheritors of the enlightenment. The trend of referring to them as thugs is a example, it brings mind someone scary that would make the reader uneasy as a person than two states clashing with the old nation likely having a massive advantage in resources, manpower, economy compared to just one province.
Two Nazi's are evil so everyone evil must be Nazis', yeah I know it's not wrong but it is definitely a thing, I myself do think it's apart of what people call the secular devil thing with Hitler being the modern one. Often times a civil war is portrayed as a battle for a nations soul, something a author will always have mixed feelings on given every nation has it's greatness and fault and often happens one side get's the bad traits and the others good, with these evil traits in turning leading to the path of the modern devil, the Nazi.
Three absolutism, AH is often great but one must admit it's got a thing for everything ending in absolutes, perfect nation or the worst nation ever ect, in other words even if they are not Nazis the rebels and loyalists will behave as if this a war of complete and total extermination from the beginning with no one doubting it's better to drown the other side in their blood if need be to win. Complete victory or complete destruction is all that awaits each side. No one will consider signing a peace deal unless it's complete submission even if it means another war starts.
Four It must matter, the idea of a nation being neutral or apathic to it is wrong so as a result the rebels must make enemies with the whole world that way you won't have neutral.
I tend to read a lot of stuff centered on civilizations that faced colonialism so Christianity tends to come up a lot.