@retrokada

I still couldn't get the .m3u playlists to run under either of the Sega CD cores.

I know that the topic below does not talk about the same emulator, but check the suggested solution and try to do the same for the emulator you are using:
https://forum.recalbox.com/topic/25156/multi-disk-sur-sharp-x1-et-atari-800/9