Templates in UNA can do more than just control the look. For example, Lucid template adds a few extra sub-pages to Homepage, which you can edit via Pages builder. As these templates evolve, they will most likely keep adding such different features specific to each template, but it is important to understand that any extra functionality must be contained to that template - so, for example, it can add new Pages, but it will not affect the way Pages builder works - it will just give it a few extra pages to work with. If, however, the template is to bring some special functionality that's not compatible with any of the builders, it would simply have the new settings in its own settings section.