I have look up through the preferences in MusicBee I have not found an option to enable case sensitiviness in the M3u exported playlist. I have the unix path by default. Look for example this 4 song playlist:
#EXTM3U
#EXTINF:308,ALASKA Y LOS PEGAMOIDES - Bailando
../../ES/A/ALASKA Y LOS PEGAMOIDES- Bailando.mp3
#EXTINF:310,EUROPE - The Final Countdown
../../IN/E/EUROPE- The final countdown.mp3
#EXTINF:184,HOMBRES G - El ataque de las chicas cocodrilo
../../ES/H/HOMBRES G- El Ataque De Las Chicas Cocodrilo.mp3
#EXTINF:250,MANÁ - Rayando el sol
../../ES/M/MANA- Rayando el sol.mp3
You can see the second song is name like:
../../IN/E/EUROPE- The
final
countdown.mp3
While in reality in Windows is set up like:

Which basically makes that I cannot use the m3u to play my music from Linux.
I am not sure if this the standard behaviour, a bug, or something that won't be fixed. But it would be nice to get it fixed.