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I noticed something that's a bit odd: slave faction building and recruiting units not from their own faction but from their parent faction (sub_faction of). Is this really happening in RTW? I've set it so that slave faction cannot build anything except core buildings, but they keep managed to build other buildings. Do sub_faction of a slave faction captain allowed to act as if he's a captain of the parent faction?
short answer, yes.
city acts as if the parent faction of the rebel general.
In BI if you're not using all the faction slots you can set what the rebels build by making the unused slots 'dead_until_resurrected' (having remembered to disable triggers) and making the generals members of sub_faction of those 'dead' factions. For testing put slave as playable and you should be able to get in and see what they can build / recruit. Note that if you do go in as slaves that building browser doesn't display correctly for them (think its default Roman) but items available for recruitment and construction queues are correct, for what they can actually build in game.