You don't lose the outputs, they just aren't committed into Git. So for each new clone, you'd need to regenerate the outputs, but on a single clone, the outputs

You don't lose the outputs, they just aren't committed into Git. So for each new clone, you'd need to regenerate the outputs, but on a single clone, the outputs exist and are persistent in the .ipynb form of the notebook (which is not committed). You are correct that the .py version of the notebook is exactly what Git ends up tracking, with the .ipynb being essentially a build product. (Note that the jupytext paradigm does assume that the outputs can always be recomputed as a function of the inputs. I consider that a best practice, but some might disagree.)