Of related interest is my Typesetting Markdown series (skip to the later parts to see R and annotations):

https://dave.autonoma.ca/blog/2019/05/22/typesetting-markdow...

I've been working on an editor that can interpolate string variables to replace those scripts:

https://github.com/DaveJarvis/keenwrite/blob/master/docs/scr...

Many Markdown publishing systems put YAML headers into Markdown documents, which feels like mixing presentation with content. With KeenWrite you can do:

    keenwrite -i filename.Rmd -o filename.pdf -v variables.yaml

Meaning, if you wanted to apply a different set of values, you can supply a different file, without having to modify the R Markdown source. (Of course, you can always write shell scripts to concatenate the YAML header prior to processing.)