When approaching Atomic design and after client discussions and research, we jump in to Sketch. This allows us to create components (The atoms, molecules and organisms), or as Sketch calls them - symbols and reuse these across the design, keeping everything consistent throughout.
Although we design ’templates’ so that the client can see how the components look when they are stuck together, it’s at this stage that the content authors can start to see how they can cherry pick certain molecules to create their own bespoke pages. This means that even if that page hasn’t been designed by the designers, content authors have full flexibility to create pages, whenever they want, with any atom, molecule or organism in Craft CMS.
It’s also a great idea to deliver a ‘component guide' to the content author, so that they have a reference to refer to for every atom, molecule and organism that can be created. No guessing at what component to choose in Craft CMS later down the line.