Well, if you want to do that alternate history stuff... I just think there isn't much Star Wars feel if you flood it with all sorts of incomplete race Civilizations.
Eh, I prefer not to take the "alternate history" angle quite that far. I like seeing the groups fighting against their historical enemies.
If civilizations were based around the alien species, ideally there would be a handful to start with (Humans, Wookiees, Twi'leks, and maybe a couple others). Some models could be reused by using battle droids or troops that are covered head-to-toe in armor, and some vehicles could reasonably be shared between them. Using species for civilizations wouldn't necessarily require more work than basing it on governments, but it would leave the creation of additional civilizations much more open-ended.
They are deciding to build an enclave on human planet. It's an abstraction. I admit that the technology thing is a bit weird, though it could abstractly represent discovery of their home worlds... or maybe those species were always there, but only become worth of mentioning when some technology they are especially good at using comes to light.
Now that I think of it, what would a city without any religion/species represent? A colony of droids? Maybe there shouldn't be a Human "religion," and just assume Humans exist on all planets.
On the other hand, maybe technology doesn't need to be the only way to discover these "religions." Goody huts? In the model some civs start with certain species.
Having goody huts contain a species envoy is a great idea.
But there wasn't really people practising "Jedi Religion," except the Jedi themselves. The only example I can remember offhand about common folk having any sort of Force Religion would be Exar Kun's Massassi. I'm sure there is a couple of more, but the point is that usually people are totally out of the loop. They are either ruled, protected or ignored by their freaks and their opinion doesn't count for much.
I don't know, the Empire focused a lot of effort on publishing propaganda about the Jedi. If the population's opinion didn't count, I doubt they would spend so much money trying to influence that opinion. While the general population did not directly practice any of the religions, they did generally support or oppose them. I would consider the spread of Jedi/Sith/whatever religions to represent the spread of positive opinion/respect for them, allowing temples and academies to be set up with the approval of the general population.
Oh yes, I agree that there's a lot of change in the Order over the millenia. Old Republic era Order was more vital and free-thinking than the stagnant Order of Rise of the Empire era, and the one started by Luke Skywalker was different again. This isn't really an argument for or against either system, however. If one civic doesn't cut it, use more.
The only way I can see this being handled is having generic civics, such as one for spiritual guidance, one for governmental guidance, one for warfare, etc. It's not feasible to have individual civics representing all the different states of the Jedi Order, then additional civics for all the states of the Sith, etc. There would be at least a dozen different civics, which seems unnecessary since all the different Force religions fulfilled pretty much the same role anyway.
I just can't see the history of the Republic being accurately represented (moving from Jedi counselors, to Jedi warriors, to Sith governors, back to Jedi protectors) without using the normal system for religions: having religions being roughly the same but separate, being able to switch between them, and having the religion's role be determined by a civic. Unless you have one civic category defining the specific religion (Jedi, Sith, etc.), and another category defining the role; in which case you're basically reinventing the religion system (only differences being there's no religion spread, you'd have to do some re-coding to allow a civic to unlock buildings/units, and you'd be cramming an additional category into an already crammed Civic screen). The normal religion system just seems like the most efficient path to me.