So I have been experiencing some weird lag/dropped frames on my Pi 4 in all Retroarch cores when threaded video is enabled that I had never experienced on my Pi3b+. These issues are extremely apparent in fast paced side scrolling games like Super Mario Bros, Mario World, etc.
It took me a while to troubleshoot and Identify the issue as threaded video in Retroarch, especially since when I would try to change the setting and save the config within Retroarch, Retroarch would crash and then not save the settings. I tried to modify the retroarchcustom.cfg located at /userdata/system/configs/retroarch to just have video_threaded = false but the modified file would never stick and video_threaded = true would always be set.
I ended up having to modify the files at: /usr/share/batocera/configgen both files configgen-defaults-arch.yml and configgen-defaults.yml to have video_threaded: false
This fixed my issues.
Just posting in case anyone else with a Pi4 is stuggling with this issue.