Obviously we do add markup to the output of the page, but it’s not through specific php files that we add and have override files already present in themes. We don’t provide php template files for anything, and I’m personally doubtful we’ll change that.
We do provide all of the output we add to say a shortcode, which is parsed and displayed via something like the_content() or if one is fancy, do_shortcode(); but it’s the user and the user’s theme that controls where those parts are displayed and they will be in the confines of the surrounding markup that the user has complete control over. Same thing with the widgets we use.
I will agree however that there could be some places that need better filters or a “pre” version that simply passes in the data that would be used to construct the markup. However I also know some of this stuff has need for specific attributes, primarily anything that’s widget based.