I don't think that there is a way to do this OOTB. The whole point of private checkout is to be able to test changes only as the specific user that you are logged in with. What is the requirement here? I guess that you want to use the same user to edit rules in private checkout, but continue to use the same user to use the system with the original functionality? I would say that using another user would be the way to go really.
Do you need to keep the rules checked out at all? You can use the checked out rules bulk actions functionality to discard all the rules that you have checked out if you don't want them checked out.
Otherwise I think marking them as unavailable is probably the way to do it, but you would need to be careful that they don't accidentally get checked in as unavailable. You could create an activity to loop through the checked out rules and set pyRuleAvailability to "No" as a custom bulk action.
How about looking at branch functionality? If you had a development branch then you could use the same user and switch between the regular application and a dev version of the application with branches for development.