From: Melbourne, Australia
This is a feature called Quick Turnaround. It's purpose, basically, is to model high intensity, multi-sortie ops that are followed by a stand-down period. Fighters, ASW and CAS aircraft are the most common units that operate like this in the real world.
In the example you describe, you are pretty much spot on with your description of how it works. The first mission--in this case--does need to be 2 hours at the absolute maxiumum, otherwise the 'average sortie time' will be over the limit. With higher sortie numbers the algorithm is a bit more forgiving. And no, it's up to you (for your units) or the scenario designer (for the AI) to make sure these units go home early in order to maximise sorties. From an AI perspective, air intercepts usually work well with this (go fly a quick mission and come back), but you can tweak patrol missions using joker settings and get good results too.