As to control interface, it may be a specific square inside command center. Then the defense tactics could look like: aftfer emergency closure of BDs, all but one defenders reaching their emergency positions and prepare. One remaining soldier (self-claimed "base commander") receives a reports of another ones and enters the "special square" for simultaneous opening of BDs when defenders are ready.
A similar thought occured to me as well. One soldier stationed in the command centre might provide you with access to a menu which provides control over the various defense systems of the base, including automatic turrets, proximity traps, etc... Alternatively, the menu could be accessible as long as the Command Centre is intact to minimize complexity (you ARE the commander after all). Either approach would confer the CC with even more tactical importance, and make it a truly critical facility in a base defense.
]Hmm, good point about the Command Center thing. Though, really, most of the facilities are senstive. Unfortunately I don't think selective spawn points is an option. Instead, though, your team could be spawned randomly throughout the base, and then given a few turns to get into position before the aliens arrive? That way the aliens can be spawned randomly, while still allowing the player to position his defenders. I think delayed spawning should be possible; there was some talk of it in the form of reinforcements some time ago. If the invading UFO is not detected before landing, there would be less delay and such.
While it's true that there are many sensitive facilities, the Command Centre is amongst the most important, arguably second only to the power plant.
That said, I do like your proposal as an alternative to selectable spawns, and it would certainly be my choice in the event that selectable spawns cannot be implimented.
The primary problem I see in implementing defensive structures is the lack of space. If the grid were to be increased to 6x6, or some other method of expanding base size at player expense, these may become more viable. Looking at the base battlescape pieces, I can see why building down may be out of the question. Now, if there was a way to implement "in-between" pieces, tiny hallway modifications that fit between the base rooms, there could be a way to implement some static measures. Security doors, cameras, motion alarms, and maybe some sentry guns of some sort. I can kinda see it all being arranged in an overhead map, with clickables for the doors (supposedly controlled by the base commander from the Command Center, though still only toggleable once per round to prevent abuse).
I've never found finding space to be too problematic, as I'm quick to build multiple specialty bases (this is a highly effective strategy, I strongly recommend it), dividing roles amongst these. Effectively the whole proves greater than the sum of its parts, or a smaller number of diversified bases.
In either case, I'd definitely say that the tactical benefits a designated proper choke would offer certainly makes it worthy of a precious tile, in that it should easily allow your troops to repel all but the most severe invasions, while offering considerable resistance to large scale assaults. Personally I'd use it without question.