Hi,
point 5) - The Bias factor on FMC is meant to cater for over all degradation. its a fuel milage offsetting factor. So it caters for engine as well as airframe(and other factors like wt etc).
point 6) I am not sure if the FMC will accept it or not, but thrust will be of the flat rate, and such assumed temp will have no benefit (of thrust reduction)
Hope it helps.