I'm on 13.19.6 and I just installed your script. I only added this part to make cleanup easier later.
function OnDeleteScript(deleteScriptData) {
DeleteVariables();
Script.vars.Delete('*');
}
Then I changed several config values (including the Global Opacity you mentioned). I tried resetting Opus (via dopusrt), exiting, and reopening Opus. I did this at least five times. In all tests the changes stayed.
Note that I only changed config values to test whether they'd stick ( and they did). So no actual use. Although that shouldn’t matter for what you’re suggesting, maybe someone else actively using your script can confirm whether they see the same problem you mentioned?