R CMD …

I see a lot of references to R CMD on the command line. Can I assume that the R in question is the R executable in Contents > MacOS within R.app?

No.  The one that will run on the command line is the one returned by 
"which R".  On my system that's /usr/local/bin/R, which is a soft link 
to  /Library/Frameworks/R.framework/Resources/bin/R, a shell script.

The one you see is the GUI front end, and it doesn't understand the "R 
CMD ..." type of command.

You can run the shell script version from within the GUI using

system("R CMD ...")

Duncan Murdoch