Ah, OK, yes I was talking at cross-purposes to some extent then, thanks. (Jupyter notebooks are hopeless in version control due to the JSON format, but I'm not familiar with Rmarkdown notebooks -- do you get sane diffs?)
Yep, so what you say makes sense. Isn't it sometimes a bit overly prescriptive to assume all collaborators use Rmarkdown? (Perhaps not! I used to work in biology and statistics and R was very ubiquitous.)
Rmarkdown indeed makes sane diffs, it's just a nice text-based format. You can use python or julia as well (see quarto.org for the latest version of this). Getting collaborators on board... yeah, that varies.
The point is that it makes sense to mix english prose + code to e.g. produce tables or graphs, even if most of the heavy lifting is done separately in code files.