Hi again Jan,
The short answer: make it for both, for the non coder and coder alike. Offer an enable/disable tick switch so that the packaged function for indentation and pagination would be available. If the packaged functions do not work right off for a particular theme, then do not enable the built in template. Design it for pages which does not have any DIV tags populated by the WP Template/theme.
About the Infinite Scroll Example:
The infinite scroll I think would be a nightmare on earth.:) There needs to be some kind of formatting (relief) for the responses like indenting, otherwise, it just a bottomless pit that would even make a seasoned mountain climber dizzy. (haha)
Using a Template which does not populate the use of the DIV tag within the page container
If you allow a plugin like Ether Content Builder to manage a the content of a page instead of the packaged template/theme, I see where possibly your plugin would fit neatly within Ether Builder as a WP module/widget. This would mean that the supplied CSS and templates for both pagination and indentation of replies for comments, could be managed by Ether Content Builder.
Ether is built on the bases that page content stay empty of template DIV tags, no columns. Each page is the canvas to set multiple columns using Ether Content Builder. The WP template/theme would only need to stay out of the page container. In setting up a WP template/theme you would set columns to: none.
Based upon that policy, the template for setting commenting would not intrude on the WP template which keeps the template's DIV tags out of the pages and therefore, the results would be consistent. The WP template or WP template engine simply manages the header/footer/wrapper areas. Ether Content Builder manages the page layout, page composition, (using TinyMCE) WP widgets (placed anywhere on a page) and Ether Content Builder's modules. The template used at Talking Manuals is not managing the page container, Ether Content Builder is managing the majority of that site.