Oh, I see. Instance PRM files are not directly supported in the custom folder. What you have to do is place a custom .fin (Instances) file in the custom folder that references ptree2.prm or podium2.prm for example. You can do that with the Blender add-on (
https://re-volt.github.io/re-volt-addon) by importing the .fin file of the respective level, renaming the .prm file names in the outliner (object list on the right) and export the .fin file to the custom folder.
Or easier: Keep two installations of the game, one modded and the other left unchanged.
If you only want to keep one game binary, you can also keep game files and the game executable in separate folders and then launch the game with
rvgl -chdir /path/to/modded_game_files
or
rvgl -chdir /path/to/unmodded_game_files
More info on launch params here:
https://yethiel.gitlab.io/RVDocs/#launch-parameters
The original purpose of the custom folder was to allow per-track customization of core game files (sounds, effects, skyboxes, user interface, ...) and also maintain compatibility with older versions of RV, that's why level instances weren't added.
I'll look if there would be any problems with adding support for PRM files in the custom folder.