I second emacs-org mode. It is extremely powerful though I don't know if it addresses GPs concerns. You could just execute the compiler etc against the actual program from within the code block and then "+CALL" in other sections to avoid the copypasta'ing I guess. I don't do very advanced stuff so I haven't run into problems with just using code in the blocks.

The main problem with emacs org-mode is that users probably need to use emacs, and lots of people have their own editor preferences, and while some have org-mode-alike's, they aren't as fully capable as emacs org-mode. Which is what Jupyter addresses by making the interface more accessible/editable to all.

That said, I think one of the most important factors that the linear notebook flow encourages is a focus on reproducibility, whether it's Jupyter or Org-Mode. I feel like overcomplicating the dev environment would make the much harder and would at least need to be planned for.