I also definitely hope the Taiping get their own bespoke Christian sect, because Hong Xiuquan was a little crazy, believed himself to be Jesus' little brother, and probably the only Christian texts he had read were garbled, poorly-translated, and otherwise inaccurate, so it very much doesn't fit as any type of Christianity that's already represented in-game.
My understanding is that while you are absolutely right on this, it didn't prevent him supporting other Chinese Christians and getting support from them. Hong embraced Arianism at one point, and yet local Chinese Catholic and Protestant communities still fought for him.
It's difficult to know how this should be modelled. Clearly, flattening all forms of Christianity into one isn't useful, but otherwise it might be quite difficult to represent this sort of "eh, close enough"-ness.
I think this is exactly where the flattening causes a problem, though. These pogroms were not enforcing Confucian religious practice qua religious practice, they were a violent reaction to perceived foreign takeover of society as a whole and a percieved threat to the legitimacy and power of elites. You can see this level of violence in pre-modern periods directed against Pure Land or Chan Buddhists when their temples acquire too much wealth or power (c.f. basically any classical wuxia film), and you can see it in the very modern period with the Falun Gong. The problem is never the dogma or practice of the religion itself; the problem is when the religious organization can generate political power and becomes a threat to the state. Nobody would have cared about Hong Xiuquan claiming he was Jesus's younger brother, had he kept that to a weekly prayer meeting and didn't start the single most destructive war of the 19th century over it.
And on the flipside, while the Taiping was ostensibly a religious rebellion, it was really more over the rapidly collapsing taxation structure of the Qing state, ethnic reaction to the conscious Manchu expressinons of domination over southern Chinese ethnic groups (the tonsure, etc). The religion provided a focus point but it was not a rebellion against Confucianism, it was a rebellion against the Qing.
While it is undoubtedly true that this is a distinction without a difference when there is a mob in the process of killing you and your family because you had a crucifix. I do think it matters when you're modeling these systems as a whole, especially when China is such a huge portion of the population and market of the world.
I absolutely agree with you about the causes of the rebellions: while religion was a useful source of cohesion around which such things could be organised, the real causes were generally economic and social. (This doesn't mean that people didn't blame religious minorities for it, of course.)
However, the life expectancies of the individuals during and after such events frequently
did depend on their religion, and usually in a very flattened way. If you're a Shi'a Muslim in Yunnan after the Panthay Rebellion, you'll still get killed during the massacre of Sunnis. If you're a Chinese person who's adopted a syncretistic mix of Christianity and Buddhism, then in the aftermath of the Heavenly Kingdom you'll still get treated as a potential traitor by the state, as much as if you were 100% Christian.
As such, I think we have to ask "what does in-game religion represent?" To me what it represents is "will this pop get affected by event X / circumstance Y?" In such a case, some flattening is good because it makes scripting easier for the developers and more comprehensible to the players.
By contrast, if what it represents is a more aesthetic side of the game where you just want to look at your population and say, yes, this looks like what I think it should, then having a less flat representation of religion which allows more syncretism and special circumstances would be good.