This seems to me like beasts of burden will just be one option, also able to be used when there is no track.
I got the same impression, namely that he'll be piggybacking BoB behaviour onto the minecart code and decoupling it from the necessity for tracks. I should hope he leaves the question of how to apply motive force to the cart an open-ended one, ranging in options from dwarf/BoB hauling, the "pump-cart" engine, mechanisms on the tracks, gravity, flowing water over the track, catsplosions, or even slave labor.
My question is, can minecarts that are explicitly hauled rather than rail/pump powered be taken off the rails? Since BoB's won't require tracks for their hauling routes, it seems like this would be a logical extension of his "define the stations, let the BoB pathfind" strategy. Maybe allow a dwarf to have a rail/de-rail cart job at stations. I can easily envision a precisely engineered rail system run on gears, powered by waterwheels, and running to major areas of the fortress, with carts being pulled to and from rail stations by cart-hauling dwarves (seperate job, maybe?) or BoBs who take them out into the mines/forests, fill them with stone/wood/silk/sand/goblinite/etc, then drag them back to the nearest station where they're whisked off to processing.
I sincerely hope we get a new type of drawbridge with built-in rails. Also, I think having a separate internal and external rail-system, connected by air-locked stockpiles between adjacent internal/external stations, would be the safest way to have the efficiency of a rail collection system without compromising security.
I expect that we won't have carts/beasts automagically loading/unloading themselves, but that's what peasants are for. If they can't be explicitly assigned to load/unload from a station, just burrow them there with only hauling tasks enabled.