The most basic and fundamental task that CJT is developed for, is to allow assigning a piece of code to WordPress pages/posts.
Creating a separate small plugin might be a good solution, however the user has to identify visitor requests and find a way to associate the parallel code. Also when reassigning the code to different pages/posts, updating the plugin would then be required.
CJT is doing all of its functionality behind the scenes. It not only takes the responsibility for identifying the request and running the code, it allows users to manage and organise their code. This is what gives CJT users the chance to clear their headspace from all the other complexities and just focus on the model they wish to create.
Not all users are able to create a WordPress plugin – even a single line WordPress plugin. Some users prefer not to deal with the technical things like connecting through FTP and dealing with programming editors. CJT solves that problem by providing a simple UI that would be easy for most WordPress users who know the basics of making a web site.