I think most FS programs include BS because it simply builds more strength - like you said, often the limiter of the FS is more related to trunk strength/stability than leg strength. That said, if someone is sound in the FS, you can pretty much substitute FS for BS - although I would never get rid of BS long-term unless it was to work around some kind of injury or limitation.
Generally I stick to 1-3 reps in the FS, but I have had people do as many as 6s - it's cruel.
I don't know that I can just give you rationale for FS programs generally - maybe if you point to a specific one.
As far as assistance work for the FS goes, I would say the BS and cleans. You would be surprised what a bump in the BS will do for the FS and clean - IF the athlete is dong the BS properly (e.g. not doing something like a low-bar back squat - in which case the problem lies there, not in an FS program).