Well, Spark can help you set up everything very fast. However, that doesn't mean you're stuck to that implementation. Spark itself is a frontend that uses the available API. You can build your own frontend components on that API. This way you can still have the same functionality but in your own way.
You maybe heard about flareapp.io. This application is built on the Spark API with a custom frontend.
Anyway, it depends on what kind of application you're going to build. If you're going to build a large SaaS it might be better to build it from scratch. If it's a small application, Spark might be a better fit ;)