I have tested a workaround for Kodi on Recalbox. It is a pretty simple hack, but it works.
I haven't looked at the script you are using to launch Kodi on RetroPie, so I can't give you specifics, but I can give you a general idea.
In the script that runs Kodi, right before you run 'kodi-standalone' (at least that's what I think the executable is called), you would add 2 lines.
sudo service fbcp stop
/home/pi/Freeplay/startfbcp.sh &
You would make /home/pi/Freeplay/startfbcp.sh look like this (and it would need to be executable).
Code:
#!/bin/sh
sleep 3
/etc/init.d/S13fbcp start
The idea is to stop fbcp, start Kodi, wait 3 seconds, start fbcp. The user won't even notice that it happened, because Kodi takes a few seconds to boot up, anyway.