Yes, because the userdata folder only contains platform/architechture independent data. So it is possible to use a copy of the userdata for every platform/architecture (PC, RPi etc.) and that’s why many poeple recommend to have seperate drives for booting into batocera and store games/bios/saves (userdata/share folder) etc.
This way, if you have trouble with Batocera, you can always reflash the image on the drive, which you use to boot batocera from and it does not whipe the userdata (roms, bios, saves etc.), which saves a lot of work.