I see lr-hatari can load an .m3u to allow disc control from retroarch. It will be automatically read from an uncompressed zip along with disk images.
Edit
It won't work within a zip, but works great loading directly from an m3u. Also, the disk image extension cannot be changed (eg. .disk1).
I changed the disk extension to uppercase and removed it from es_systems.cfg
I suppose you could use a hidden folder as well.