Sorry, but I am not sure to understand the issue.
Non R code block will execute using the correct executable provided in chunk options or found in PATH I think.
See documentation in the new Rmarkdown book:
Can you explain more precisely what is the specific issue you have ?
Or better, could you ask this with a minimal REPRoducible EXample (reprex)? A reprex makes it much easier for others to understand your issue and figure out how to help.