Well, if we look at this from a gameplay standpoint, having all your troops congregated at the entryways the moment the aliens arrive takes much of the fun and challenge out of it. Now, if only some of your troops are in position and the rest are scattered, or the invading alien force greatly outnumbers the defenders, there is more potential for pitch in the battle; of course, balancing this is another issue.
The advantage I can see of having a two-part battle, one above and one below, helps justify this a bit. The top battle pits the player's current shift (the dropship junkies, for instance) and the Entrance defenses against the brunt of the invading force, with the option to withdraw troops from the "down" location when things turn sour. If the player manages to win, then the base invasion ends there. If the player loses or withdraws, the battle continues in the lower sector.
The lower section allows the player to replace his dead and wounded defenders from any other troops in the base. The next battle involves defending the remainder of the base with the second group. Perhaps the aliens could have their spawn delayed until the player takes his first turn. Should the player lose, the base is overrun, the remaining personnel are killed (or captured, if there is any game mechanic for which this would matter), etc. Winning the second phase keeps the base alive, but the upper section could be razed, with the facilities requiring time, money, and possibly worker time to repair. Ships may be damaged/destroyed as well, etc...
The idea here is that the first battle will be incredibly difficult to win, and the player must decide whether he can hold out another turn, or if he has to withdraw to cut his personnel losses (in the hopes he can turn it around in the second battle).