His entire arm might not have died, and perhaps Lucrecia or Hojo wanted to keep as much flesh as possible. They may have removed the dead tissue and added that 'claw' part as the rest of the arm and perhaps as a little tissue preserving unit to keep the little arm tissue alive.

As for the shoes, they are the furthest in the bloodstream, so they deteriate first. The 'pointed' parts are reworks of his feet, probably much like his arm.