Basically sounds like you'll find a survivor of the event that goes on for the other faction and he'll tell you a story of it, except you will be the bad guy in the story playing it out. So think Escape from Durnholde where we basically had costumes on if you didn't fit the lore. That's what's going to happen.
Also, the way he explained it, the last 3 bosses for the Alliance will be the first 3 bosses for the Horde. So basically, Alliance are the instigators, they fight their version of the raid, killing 3 Alliance only bosses and 3 neutral bosses (gold elemental is pretty much going to be one) at which point after Alliance finishes (with King Rhastakhan since he is a throw away boss to further his daughter's story) Horde shows up from the North, sees what happened with the King, then fights the 3 neutral bosses and 2 more Horde only bosses on the docks to chase the Alliance for what they've done, where it all culminates on the open oceans where the Horde fight Jaina (who will have conveniently lost all of her extreme powers she has shown over the years).
Then, after you have done your factions specific bosses, you'll get access to the other factions 3 "exclusive" bosses and get to do them in story mode basically.
It's going to be a nightmare balance wise and I can't wait to see the amount of rage when one side has a perceived win over the other at the end of it or bosses are easier for one faction.