it would offer no protection against, for instance, even a fatally inappropriate flex.
...and it is not designed to do so. As framer indicated, the FMS is not a complete takeoff performance computer. However, it CAN be used to crosscheck several aspects of takeoff performance. While the FMS may generate rough V speeds for takeoff, for example, we still use a dedicated performance computer to refine them.
Once again, you are supposed to be a professional pilot. Your knowledge of the airplane, its capabilities, and the environment should be a key factor in assessing whether any calculated thrust reduction is sane for the circumstances. Blind acceptance of automated tools is not good for your health.