1) I'm not sure about that, either. Unless the coaxial digital output is somehow linked to the zone 2, which I wasn't aware of.
2) I don't know about this one, either, unless you count zone 2.
3) The second trigger can be configured for each individual input. If it is set to "on" for all inputs, it'll trigger as soon as you turn the unit on (the remote "on" command is achieved by sending an input selection). I guess the one time this may not fly is when you push the power button on the front panel, but even then the trigger is tied to the input last used and will come on right alongside trigger 1.
4) I believe that "on the fly" changes are saved.
5) Both balanced and unbalanced outputs are active at all times, so this would be possible.
Sorry my first two answers couldn't be more informative...