@idemiq hello. Apologize for reopening that thread but I like when solutions are found whenever possible! CD32 is a bit tricky to get working but the good news is that it works!
Can you try renaming your .CUE that way and give it another try? Do not modify the .bin file or any other file(s) referenced inside that .cue.
AlienBreedTowerAssault_v1.2_CD32.CUE
Your Kickstart roms appear to be correct. Yet I do see that you put these inside BIOS/amiga folder. I'd recommend to just go with BIOS instead. Therefore move any KS file up to the BIOS folder of Retropie and delete the BIOS/amiga folder for now. To be sure.
Also after you renamed the .CUE and moved the KS roms as mentioned above, please ensure to delete any .uae you have generated (back them up somewhere else if you want).
If the above works then you'll have to rename the .cue the same way the games are being referenced in the whdload_db.xml file (search for CD32). Which you could find under <Retropie>configs/amiga/amiberry/whdboot/game-data.
Hope this helps.