When you destroy a building (defined as taking its HP down to zero), it displays a lengthy death model (usually) and until it fades away, the unit isn't truly considered dead. Thus, as a result, when you destroy the foe's base completely, there's a few seconds of doing nothing after you destroy the last building. GAE solves this by having the game end the moment the last building's HP reaches zero, and MG should do the same.
Of course, most likely to be merger content, though worth pointing out all the same.
