I know only a Rube would ask this questions but I have never had a Stack Battery Mod.
If I place two Freshly charged 3.7 volt batteries into this mod then Output of the Batteries should be about 8.2 volts. And if I set the Mod to be say 4.0 volts, then the Mod will run until the Voltage of the two Batteries reaches 4.0 Volts.
Correct?
No, for this type of device and any "buck" regulated mod that uses 2 batteries you will find that fresh of the charger you'll start at closer to 8.4v and it will run down to some point where the mod decides the batteries are to low to provide good output and at a point where you will not hurt the battery life by running them too low. Often this will be someplace between 6 and 7 volts (no load) which would be 3.0 to 3.5v per cell and probably as low as you want to run them for long life.
Unregulated mods using stacked batteries are another story and can potentially run batteries much lower.
This mod will flash "Lo" occasionally under load as the batts run down but will still be entirely usable till the "Lo" flashes about 1/2 of the time u r on the fire button. On this device where this depends on the resistance of the load and the voltage setting because the more load u put on it the more the voltage drops under load and triggers the "Lo".