I appreciate the effort you've put in here, but I'm not keen on recapitulating savehist-mode inside org-gamify. A bespoke persistence mechanism is really outside its scope.
Emacs needs a better solution for persistent variables. Savehist-mode provides most of the necessary functionality but it doesn't handle some corner cases such as your need to finely control which variables get saved where. Can I suggest that you consider submitting a patch to savehist that allows the user to specify that certain variables 'live' in particular files. This would both solve your problem and make savehist a more useful general persistence facility for Emacs.