Sound blaster 16 has no internal midi.

Perhaps Windows 3.1 has better OPL3 midi emulation?

In order to play MIDI on a sound card like the SoundBlaster 16, you need to map the MIDI instruments to settings that the playback device (usually an OPL chip) can understand. A MIDI file can sound differently on the same hardware, depending on what software was used to play the MIDI file (and how the software maps the MIDI imstruments to OPL settings).

I can only guess that most MIDI players under Windows use the Windows API/drivers and let Windows process the MIDI events and convert it to OPL-compatible data. It is possible that the MIDI player from your SoundBlaster disks accessed the hardware directly, so it had full contol over the instrument settings, resulting in better sound quality.

OP's referring to the Voyetra SuperSAPI drivers that were shipped on the original SB16 floppies back then (they were not compatible with Win9X nor NT). It was still OPL3 but are more complex timbres etc. Having SuperSAPI available in a more modern 32-bit form has been a white whale of many here for years.