-Do I loose all the setback settings if the power goes out? I do have it hooked to a backup power supply for now. But if not?
Setpoints (temps and times), SETUP menu items, etc. will all be remembered indefinitely regardless of length of power loss. Time (and day, if a TS1) will be forgotten and you'll need to reset them. If the power loss is short then the time before the power loss will be remembered and when power is restored the time will pick up where it left off. The clock will not run during the power loss, though. I'm sorry, but I don't recall exatly how long it will sustain the time during a power loss. At least 5 minutes on TS1s. On TS2's it can be substantially longer, several tens of minutes if I remember right.
-How does it know if I have a flame out, is there logic that if the thermostat is not satified within a certain amount of time, shut it down or stop the stokers? I know I read you have OVERTEMP in the room.
Currently shipping units have no logic for stopping the stoker or otherwise detecting if the fire is out. In the software that's in development which supports fully automatic ignition we do have this kind of logic in place. In this case it was primarily to reattempt an ignition, but it is also used for the purpose you describe.
-Any future inputs for maybe a temp. switch or temp probe to check exhaust temps for flame out? Turn the stoker off if below a certain stack temp?
We have some early prototype hardware that supports additional temp probes and other sensors at the stove, but no idea when or if it would ever make it into a retail product. More likely we'd integrate the before mentioned code logic into no ignitor and manual igniter modes.
For now your best bet for the kind of "safety" you're talking about would be to wire the a low limit switch inline with the stoker (or perhaps run main power box power feed through it) to prevent feeding if the fire went out. However, you'd need to be careful that it doesn't interfere with stoking during fire starting or minimum fires. Probably would require a manual reset temp switch (or a toggle switch wired in parallel with the temp switch, as a bypass) so that you could force the circuit closed when starting the fire.