I think it's quite unfortunate that they did not consider that the format would integrate well with version control systems when first designing ipython notebooks.
If you give me a counter example, good for you, but my statement holds true 99%.
But you are saying here: "If you leave git diffs in your files, whether Jupyter notebooks or otherwise, and run/compile them... They will break."
Have you changed your mind in this thread? Or what's your objection?
But if you don't know that git modifies files when conflicts, then you're an interesting and rather unexpected audience, I assume.
Meaning that for the typical git user, meaning, knowing about git diffs, the behavior is expected hence not broken. The files end up in an expected broken state, but git does not break them per se.
If you still disagree, let's just settle that we disagree and be done with it.