I have just found out (using mapview) that navigation blocks in alien base control room have following flag:
special properties: DestroyObjective
Looks like the game logic is quite simple, so you can move these blocks around, add more or whatever. The game just checks whether all of them are destroyed. May be i even can test this
I would really like to see some variants of base control center, maybe more defensive and more dangerous for x-com soldiers. Several sequrity doors, close quarters, small lifts, objective blocks in different rooms...