Im not the best person to answer this in detail, but I belive that in a single mission, 2 out of the 3 campaign layers are also loaded up along with what ever you scripted your self.
One of these is LND layer which contains all the airbases, you will never physically see an airbase as its an invisible radius that will randonly spawn aircraft within it - when an enermy unit (ie - the player) is detected.
So yes - random units will still spawn in a single mission. And yes units can call in other units to hunt you down, not sure exactly how it works though.
Its funny but I find that the more you learn about the mechanics of SH3 and how the world actually works, the more 'magic' you lose from the actual experience of playing it, i think ignorace is bliss in this case.
