ok this was an easier workaround than I thought…
just go into console and mount the title:
cd /userdata/roms/ps3
mkdir SomeTitle.ps3
mount SomeTitle.ps3.squashfs SomeTitle.ps3
Update your game lists and boot the mounted copy [for whatever reason, it won’t show up in RPCS3 config on its own]
Then go into RPCS3 config and you should see the title in the game list and right click it to “Create Custom Configuration” (be sure to “Save custom configuration” in the corner)
when you’re done, be sure to clean up:
umount SomeTitle.ps3
rmdir SomeTitle.ps3
refresh your game lists and your custom config will persist because it’s associated with the game ID.