For batocera use S99Custom init script

I wouldn't change the init.d/s99custom. If you look in that file it calls to the shared mount to execute a custom.sh file. You make your changes there.

Here's a fully working install file. Just paste the below into a new batocera_install.sh file. Then SFTP it to the box, make it executable and then run it. Everything works as expected.

#!/bin/bash
#Step 1 make /boot writable---------------------------------
sleep 2s

mount -o remount, rw /boot
mount -o remount, rw /

#Step 2) enable UART and system.power.switch----------------
File=/boot/config.txt
if grep -q "enable_uart=1" "$File";
    then
        echo "UART already enabled. Doing nothing."
    else
        echo "enable_uart=1" >> $File
        echo "UART enabled."
fi

sleep 2s

if grep -q "^system.power.switch=PIN356ONOFFRESET*" "/recalbox/share/system/recalbox.conf";
    then
        echo "PIN356ONOFFRESET configuration already enabled."
    else
        echo "system.power.switch=PIN356ONOFFRESET" >> /recalbox/share/system/recalbox.conf
        echo "PIN356ONOFFRESET configuration enabled."
fi
#-----------------------------------------------------------

#Step 3) Download Python script-----------------------------
mkdir /recalbox/share/scripts;
sleep 2s

script=/recalbox/share/scripts/SafeShutdown.py

if [ -e $script ];
    then
        echo "Script SafeShutdown.py already exists. Doing nothing."
    else
        wget --no-check-certificate -O  $script "https://raw.githubusercontent.com/RetroFlag/retroflag-picase/master/recalbox_SafeShutdown.py"
fi
#-----------------------------------------------------------

sleep 2s

#Step 4) Enable Python script to run on start up------------
DIR=/recalbox/share/system/custom.sh

if grep -q "python $script &" "custom.sh";
    then
        if [ -x $DIR];
            then 
                echo "Executable S99RetroFlag($DIR) already configured. Doing nothing."
            else
                chmod +x $DIR
        fi
    else
        echo "python $script &" >> $DIR
        chmod +x $DIR
        echo "Executable S99RetroFlag($DIR) configured."
fi
#-----------------------------------------------------------

#Step 5) Reboot to apply changes----------------------------
echo "RetroFlag Pi Case Switch installation done. Will now reboot after 3 seconds."
sleep 3
shutdown -r now
#-----------------------------------------------------------

RetroFlag / retroflag-picase

For batocera use S99Custom init script #14