EDIT: i maybe didn't test enough -- the "remaining values are filled" in the .conf, only when run the +Start Amiberry.sh. When launch by one of the .lha roms instead, no values are filled, but the game still seem to work. They load and play anyway, did not test saving. But it's late and I've shut down for the night. Will test saving tomorrow.
Yes, saving works:
pi@retropie:/opt/retropie/configs/amiga/amiberry $ cat conf/amiberry.conf
rom_path=/home/pi/RetroPie/BIOS/amiga
floppy_path=/home/pi/RetroPie/roms/amiga
harddrive_path=/home/pi/RetroPie/roms/amiga
cdrom_path=/home/pi/RetroPie/roms/amiga
lha_path=/home/pi/RetroPie/roms/amiga
pi@retropie:/opt/retropie/configs/amiga/amiberry $ ls -l whdboot/save-data/Savegames/ItCameFromTheDesert/
total 16
-rwxr----- 1 pi pi 12444 Dec 20 11:36 ICFTD
pi@retropie:/opt/retropie/configs/amiga/amiberry $ file whdboot/save-data/Savegames/ItCameFromTheDesert/ICFTD
whdboot/save-data/Savegames/ItCameFromTheDesert/ICFTD: data
...save file exist, and I can quit and restart amiberry, then re-load the save in-game.
It's the same with either github/retropie version binary: no values are written (and file NOT created) when loading from .lha rom, saves still work at default location. Values are written (and file is created, with github version) when launch from +Start Amiberry.sh.
Edit: Launch from .lha rom, then open amiberry config and change eg. Rom path: all values are written to file (for both RP version with minimal conf, or github version with no conf.) But, if open config then quit with no change == no write values.