One of the main problems that I see from Batocera (other people will see it as an advantage, I cannot agree),
its unpacking itself at every reboot over the full file system. Now, not only you have writing your support (sd,ssd..)
at every boot, so it can wear out your support. This was not the case with Recalbox 4. So, if you want to make modifications on Batocera (without modifications on Recalbox I would have never arrived to adapt Recalbox to the Freeplay GBA), you must recompile your own version, not really a solution.
So, apart from the wear out by writing access on the system files (often USB stick) and not only to the Share part,
there is worse.
Because exactly from 5.20 on, dolphin and perhaps other configuration files are also overrided in your share folders. This is absolutly nonsense. Imagine Windowsxx modifiying your accounting, mail, commercial software running under windows. There would be war in Seattle.