The first one takes place just after "In a Mirror, Darkly", so they'll have the Defiant (though won't be able to build more until researching the tech needed to build it normally). Soval will have magically risen from the dead, as I don't feel like inventing a new leader for the rebels.
Those scenarios will be unique in that they will essentially be pre-defined starts on the regular game with custom civs/units. You'll actually be able to tech up to the end of the game normally.
Might as well post the rest of 4.0's design doc while we're at it:
Scenarios:
-Mirror: Rise of the Terran Empire (2155, turn 35)
--Terram Empire (Sato), Rebellion (Soval), Tholians (generic), Klingons (Duras), Romulans (Valdore)
-Mirror: Fall of the Terran Empire (2280, turn 94)
--Terran Empire (Spock), Cardassia (Skrain Dukat)/Klingon (Chang) (team), Romulus (Nanclus), Tholia (generic)
-Mirror: The Terran Resistance (2373, turn 270)
--Terran Resistance (O'Brian), Alliance (Worf), Romulus (Neral), Tholia (generic)