Yeah, the m3u thing will only work for certain emulators and platforms, unfortunately. I agree that it is the best solution for those platforms though, so we'll probably add an option for that at some point. Putting out a new beta now. It's a one-liner, but it should really help with multi-disc imports:
- Improvement: Importing multi-disc ROMs that are named correctly with (Disc 1) or (Disk 2) will now stop importing duplicates and create the extra discs as additional applications instead