beamer-theme-matrix | Shows variations of the Beamer LaTeX package

If I understand the rmarkdown lingo correctly, they use the term template for the instructions how the markdown document will be translated into tex, e.g. the default beamer_presentation template for example defines how information from your yaml-header is used in the tex document, e.g. that whatever you put down for title will be translated into \title{...}. It also contains a hole kitchen sink of packages rmarkdown loads by default, many of which make no sense with beamer.

the include hooks offer possibilities to smuggle additional latex code into your document. The difference between the different options is where they will be executed in the intermediate tex document. For example in_header will be included at the end of the preamble. Which of them to use will depend on what you want to add. For most things in_header will be fine.