The design is optimal defensively speaking because the aliens *might* be able to make a successful spearhead and scuttle your first chokepoint (presumably at the 1st living quarters). This is increasingly likely when you're invaded with larger ufos which have more aliens (wait until the battleships and corruptors come along). In the event this happens, the advantage gained by the aliens is minimal as the ground they've won is only more valuable tactically in that it's closer to your key facilities, providing no alternate routes of entry or escape. In my experience, it's also difficult to have all soldiers properly contribute to base defense by locking down a living quarters module (or entry module for that matter), without rendering them exceptionally vulnerable to area of effect weaponry. A prolonged, continuous choke allows for reverse leap frogging if needed, and this tactic likely will be versus more numerous and powerful aliens, especially once better AI is implimented. All told though, you are right in the assessment that generally, and by and large, a single choke is almost invariably sufficient to resist an alien attack at the present time.
Also on a related note, I strongly believe there should be some sort of 'Security Station' facility ala X-Com Apocalypse, which is specifically built and equipped to be a proper chokepoint with pillbox slots, fortified walls and automatic turrets.
As for the Command Centre, once it becomes an area of strategic and tactical importance, it would not make a good spawn point for this very reason, despite any defensive characteristics the facility may have; you do not want firefights occuring there.
Lastly, while economizing space is important, typically I find I'm able to 'specialize' bases to excel at certain roles, such as research, manufacturing, interception, dispatch, etc... Specialization consequently minimizes space economy problems and monetary expendatures without signifigantly impacting overall performance.
