I'm pretty sure in regards to the music in Duke3D, it was all done on SC-88. Pay close attention to the BONUS.VOC and GRABBAG.VOC files and you can notice the instrumentation being identical to what you can find on the SC-88.
I think perhaps the SC-88pro would be a good choice since that was out around 1996, same year as Duke3D.
And yes there are various tracks that use specific controller messages meant for Roland GS devices, which I've only seen BASSMIDI actually interpret at all. FluidSynth doesn't understand these. ALIENZ.MID uses a special message to up the pitch of the snare drum that a lot of MIDI devices don't listen to and results in playing the power snare at it's default pitch. Various other of the MID's have reverb settings being applied globally.