Well, since the very beginning, Cook has been designed for the application layer. Templating is another job.
Once your project is generated, whatever is in the tmpl files, you can change it.
Maybe in the future it can become more handlable to customize, but goods HTML and CSS are needed for every layout of your component.
While the html controls are abstracted, you don't have to touch anything else than the HTML structure.
With the coming of JForms (soon), the forms creation are handled and you will be allowed to use something else than tables.