Did some updates as it turned out that a more recent ScummVM core (2.5+) in lr-scummvm does use the scummvm.ini.
My scummvm_helper.py does apply also again for the lr-scummvm, and:
When a Add Game or Mass Add... is done in lr-scummvm UI it follows the same logic as the native ScummVM:
Make unique game id entries in scummvm.ini by chopping of any variant suffix.
It creates *.svm files, if missing. The *.scummvm extension should only be used by the rom-launcher.sh internally as it might produce doubles in the gamelist if these would be enabled in es_systems.cfg.
For those who want to testdrive:
Create a dedicated <folder>, change to that <folder>. Run a git clone with the URL mentioned above at [1].
Run retropie_setup.sh / retropie_package.sh as usual in the <folder>/RetroPie-Setup