Thanks for getting in touch! When defining files to perform substitution on, any entries that exist within these files that match project variables will be substituted with those variable values. If the variable exists in multiple defined files, it will substitute in both, and unfortunately there's no way to limit that in any way. You could accomplish this by creating a unique project variable name, but that would require you to alter this specific JSON file as well. Would that be a possible solution?
Sorry it's not better news! Don't hesitate to reach out if you have any further questions or concerns going forward.