On the Publisher.. you could configure a "+" button to the right of every Product. clicking on this lets you add a SCOPE to the product/category.. or select a scope that was already added. You would also be able to remove a SCOPE from the list.. discarding any custom settings for that product/SCOPE combination.
selecting a scope on the product/category.. would create a different set of configurable settings.. which ONLY apply to devices with the matching SCOPE. just create a new INI based upon the SCOPE name.
when an application install occurs.. if it has multiple ini files.. it would evaluate its membership in SCOPE collections. to evaluate if a given ini should be used.. (1st match wins.. otherwise.. it uses the generic ini for that product)
It might be better to create a compliance rule to pre-evaluate SCOPE device membership. I didnt see any powershell commands to discover this .. since its indirectly related through collection memberships.
This would make the current SCOPE assignments in the publisher unnecessary.
As a later step.. create a sccm console extension to manage all the publisher settings. restrict SCOPE changes based upon their admin SCOPE.