No worries, ask as many question as you can, this helps you , me and everyone in this thread

Now coming back to your question: It does not matter too much, since the temperature controller will override the timer's effect on heater (whether it on or off) since it runs lot more frequently. Its just bit misleading from the timers perspective, that even though you declare it to be on whole night, it might not be, cause temperature controller may switch it off if the temperature is high , vice versa, it may turn heater on, during day if temperature is low, even though timer has turned it off in the morning.
Now, regarding your issue with the temperature controller, I just realized there was a bug and I fixed the temperature controller couple of days back (
https://github.com/reef-pi/reef-pi/pull/208/files#diff-424f58a504a5feac0bb39c17cf5950b7R126) . I'll cut a release tonight (in 5 -6 hrs from now), you can use that. Will that work?