If the bolts are just through the plastic you can remove them both (plus the claw nuts on the inside of the shell too). Just put some duct tape over the holes.
If the bolts are mounted into a metal backbone, you don't want to remove all of the bolts, just the top one. If you take them both out, the metal backbone comes off and you will lose all sorts of cuff stability.
Concerning further softening the second option, have your boot-fitter cut your shell to find the exact flex you need. The boot is designed to have this done to it if need be.