@zombiefly Ahh, sorry to hear that. To be honest, the lack of options for fs-uae-launcher makes sense, given that the goal of is to get you quickly running the game with the optimal settings already pre-configured.
You might be able to roll your own command line that calls fs-uae directly - something along the lines of:
/usr/bin/fs-uae --fullscreen --amiga-model=A500 --base_dir=/userdata/system/configs/fs-uae --kickstarts_dir=/userdata/bios --save_states_dir="~/RetroPie/roms/amiga/Flashback (1993)" --zoom=auto --floppy_image_0="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 1).adf" --floppy_drive_0="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 1).adf" --floppy_image_1="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 2).adf" --floppy_drive_1="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 2).adf" --floppy_image_2="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 3).adf" --floppy_drive_2="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 3).adf" --floppy_image_3="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 4).adf" --floppy_drive_3="~/RetroPie/roms/amiga/Flashback (1993)/Flashback (1993) (disk 4).adf" --joystick_0_left_shoulder=action_key_f1 --joystick_0_right_shoulder=action_key_return
I've not tested it, but hopefully it gives you enough to have a play and get working.