The main problem with having just one person so much in charge is that if anything had happened to me, chaos

Don't like brittle plans. I always had 40 people in mind, the only bit that I felt was a problem from that point of view was the stops.
I don't really like the designated marker system as used at the AR- main reason being you end up with markers constantly pushing through the pack to get back to the front, which isn't ideal (the red mist descended a fair bit in the last 2 I think, naming no names). It depends on the route though- like this year, there were very few junctions that needed marked at all.
The drop-off system does work as long as no idiots clear off, which isn't that likely really on a ride like this. Personally, i reckon don't mess with it- you don't need group leaders or anything like that, you just need everyone to know how it works.
I think maybe just armbands or something works for the trail bosses (I like that name, i'll stick with it)- enough to make them fairly recognisable but not enough to cause any confusion with the top and tail riders. The job as I see it's really just to jump in if there's any problems more than anything else, I think the place they'd make the most difference is at rest stops, to keep things moving, but also they can take over marking a junction if they want, stuff like that- like I say, it's what some people (you included) do naturally anyway, so it just takes that one step further. They're definately NOT just markers. I think most of the time they'd be better on the road than stopped at a junction really.