If you want to store (e.g. base64-encoded) outputs in Markdown, you're going to have to scroll past a lot of data to get to the next input cell in a notebook.

Jupyter notebooks store which Jupyter kernel they were run with to generate the outputs.

nbformat (.ipynb with inlined base64 outputs) isn't a sufficient package format: https://github.com/jupyter/enhancement-proposals/pull/103#is...

Papermill is one tool for running Jupyter notebooks as reports; with the date in the filename. https://papermill.readthedocs.io/en/latest/