Kodi?

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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.