Chris, great that you think the »cleanm« theme is a good and understandable example to work with. The work I have investigated seams to help others.
»cleanm« works with renderables and renderers. For example »class columns3_layout extends base_layout implements renderable, templatable«.
With the Moodle docs I find myself often in the same situation - abstract descriptions of complex topics which are difficult to understand without examples. The cookbook approach is much more helpful for me in many cases. I learned about the Moodle Mustache implementation much more while looking and analyzing Damyon's »learningpath« template example in his Git repository than by reading the docs.
The »partial« subdirectory I have created to save all »dynamic partials« which had been loaded with a »dynamic partial helper« in the first implementation. Damyon proposed to render the »partials« within the renderables without a »dynamic partial helper«. I had proposed to add the »dynamic partial helper« to Moodle core because I think it makes definitely sense when working with templates. But I never have gotten an answer and Moodle 2.9 shipped without a »dynamic partial helper«.
By the way - why do you think the partials subdirectory is an issue? Technically is doesn't matter if you save the templates flat or in an organized subdirectory structure. I prefer the organizational subdirectory structure to offer e better overview.