Tom, The best fork of the TwentySixteen theme specifically for IndieWeb use is David Shanske’s at https://github.com/dshanske/twentysixteen-indieweb.
The one you’ve pointed to is a child theme meant to be used in conjunction with the base TwentySixteen theme but with some IndieWeb-centric modifications that I use on my site presently. (It was also meant as an example of how to set up and use a child theme as well.) Most of the modifications for the “child” are in the functions.php file. If I recall correctly, that child theme adds in some additional mf2 properties, but not everything it should (yet). In (IndieWeb) practice, I find it works pretty well, but without some of the more drastic changes David’s more customized version does–his completely removes Post Formats in favor of his Post Kinds plugin. I wouldn’t use the child theme or David’s fork with the mf2 plugin.
In general, if a theme properly supports all the mf2 properties, then it shouldn’t use the mf2 WordPress plugin, which can cause some conflicts/problems with some themes. In fact, if I recall correctly, themes like Sempress, Independent Publisher, and David’s TwentySixteen fork specifically declare that they support mf2, and the mf2 plugin should automatically (and silently) not run so that the code isn’t replicated. The mf2 plugin has had some problems in the past because it is doing its best to inject microformats v2 into themes without knowing what they may or may not have already, thus potentially causing code duplication, problems with things the theme may be overriding, or–in cases like the TwentyFourteen theme–breaking the CSS because the theme is improperly using mf2 classes for CSS instead of for semantic reasons.
I think the current consensus about the mf2 plugin is to not use it, but instead to favor the recent https://github.com/indieweb/wordpress-mf2-feed. Instead of relying on WordPress core and the user’s particular theme to appropriately implement microformats, this plugin attempts to create a separate side file (similar to how RSS files are done in WordPress) using a rel=”alternate” link to show the proper microformats on a page’s output. Parsers that want the appropriate mark up can then use this alternate representation instead of the page itself. In general, this plugin and the side file are meant as a stopgap until there are more modern themes with appropriate support.