Matt, I did not realize any KX250 pipes fit on the KDX250. You are right that FMF shows the same part # for the'92-93 KX Fatty as they do for the '91 - '94 KDX250.
Depending on what type of power delivery you are looking for, I would consider chaning your stock silencer/spark arrestor and keeping the FMF fatty. On mine, I used an old Answer SA Pro spark arrestor modified to fit from an 89-94 KDX200.
I used to run the FMF/Answer combo on the trail, and the quieter stock silencer and pipe on dual sport rides. With the aftermarket system, the bike revved out farther and did not have an abrupt low/mid hit (jetting and other engine mods were not changed w/ the pipe switch) that was present with the stock system.