Same question - where is game data folder situated now?
According this manual https://retropie.org.uk/docs/Optimization-for-Nintendo-64/ the folder must be /home/pi/.local/share/mupen64plus/ but share folder is empty and game saves are located in roms folder....
So, where need to put hires_texture to apply it now?

@spacemonkey I assume you worked out I got the path wrong - I meant /opt/retropie/configs/all/autostart.sh - glad it's working.