Ther have been several posts that I have read and several off forum articles, touting the capability of some Tstats like Ecobee adjusting room temps based on occupancy.  From what I have been able to gleen, this is accomplished with a motion sensor built into the thremostat and room sensors.  What makes this occupancy sensor more advantageous then using a stand alone MS and if you can use a stand alone MS, is there a secret sauce that needs to be programmed in ISY for it to mimic a smart Tstat occupancy sensor?

The sensors that come with thermostats such as ecobee works directly with the thermostat. Without 3rd party intervention. This means less time programming and should the system fail, your thermostat setup still works properly

The features can be duplicated with a third party sensor however via programs. You would want it hardwired as most sensors that show temp will not update often enough to be as effective. The rest is simply a matter of programming your sensors to your thermostat to operate off them the way you want