The workflow

Restructured text works well. It has great support for tables, and with declarations and special characters such as \sphinxtitlerefsphinxcontrib.bibtex package, it works well with citations. Tables and images can be handled with R easily. I can keep the code separate and out of the way using \sphinxtitlerefoptions: strict in Rstudio.
So, write the code in Rstudio and then once happy with the code and tables, do \sphinxtitlerefknit(filename.Rrst). Note that the name of the file is \sphinxtitleref.Rrst. Knit will convert the file to \sphinxtitleref.Rst. R will also create separate folders to keep the image files. The tables are converted using the \sphinxtitlerefkable() function in \sphinxtitlerefknitr, and it works well.