GPL can make sense for algorithms, but not for infrastructure, such as an application platform. I would recommend to keep the permissive license for the application platform changes and only apply GPL or other commercial license to specific modules or algorithms that you develop.
The custom application template will help you with very clearly separating the stock Slicer core (that the superbuild pulls in), your customizations (Applications folder of CAT), and custom modules (Modules folder of CAT). If you want to save time on maintenance then you can push back some of your customizations/enhancements into the Slicer core.