B,
If you had a single speed pump, the pump would run in the Service mode, if you pushed the pump/filter button.. Since you have an IntelliFlo it will not run because in the Service mode the com port is no longer talking to the pump.. You can wish it works differently, but that is how it works..
It is your system, so you can run it anyway you want, but putting it into the timeout mode at bed time makes little sense to me..

In theory, the timeout mode should turn the system off for 3 hours, and then revert to auto mode.. But I've been told before that this no longer works.. Not sure if it is a bug or what, but since 99% of users do not use the Timeout mode, I doubt many have noticed.
In theory, the purpose of the Service or Timeout modes is so that when the "Service" guy comes by to work on the system, he can disable any automated actions.. You really don't want to take the filter apart and have the pump suddenly start up..
Maybe there is a better way to do what it is you want to do??? What is your reason for going into the timeout mode at bedtime??
Thanks,
Jim R.