I'm not seeing nearly enough differentiation amongst possible factions and among dwarves for factions to work in DF.
One problem with Tropico-style factions in DF is that DF does not yet have opposing pairs of ideologies. No Armok vs the Carp God, no communist worker's paradise vs democracy's controlled chaos.
Another problem is how to sort out what faction(s) best appeal to each dwarf. Dorfs float amongst several roles as needed, and as labors are enabled. Nobles double as laborers when not doing their noble duties. Beardy brains might explode if they try to decide what faction to support.
That's one of the reasons I proposed that these loyalties would work directly between the dwarfs themselves instead of between the dwarfs and the "entities" they are a part of (I don't think official factions are needed for this to work).
I agree that dwarfs should be able to make decisions on their own personal ideologies, as soon as these have been built on. But, I think their degree of contentment (if they like the current ruler or are afraid of taking a stand) and the ambitious conspirer's charisma (the social skills as they are now) and material resources (bribes) would be the most important factors.
Of course, like-minded people would be more likely to be allies; I think we can all agree on that. How would you construct this opposing-ideologies-system-thingy?
Took me a while to process all that you wrote. Sorry if I'm missing some important point.