Bloggs,
Unfortunately logic or indeed, even common sense failed to enter into around 90% of the procedures that were introduced after 9-11. As far as having an FA in the flight deck when one of the pilots went to the toilet, it was to mitigate there being only one pilot in the flight deck at any point during a flight.
As far as having armed pilots, don't start me on that topic. It was a stupid f*$€ing idea, brought in to give the travelling US public the warm and fuzzies.