"does that license apply retroactively to a checkout of the first N-1 commits"
No, unless you explicitly state it somewhere (and even then, I'm not certain).
If they add a license to the older commits via rewriting history then yes, those older commits will now be licensed. If they don't do so, then copyright will be default i.e. you can't do anything with it.
Now, if they had a large history and didn't retroactively license files, but just pushed the repository out all at once, I have no idea if the license on the latest commit would apply to the older commits. In the end, the question is all about whether or not Apple has the legal ability to sue you for copyright infringement.
Is there any legal precedent for this? It seems like one could make a reasonable legal argument for either interpreting a repo as a single distribution or as a bunch of separate ones.
No, unless you explicitly state it somewhere (and even then, I'm not certain).
If they add a license to the older commits via rewriting history then yes, those older commits will now be licensed. If they don't do so, then copyright will be default i.e. you can't do anything with it.
Now, if they had a large history and didn't retroactively license files, but just pushed the repository out all at once, I have no idea if the license on the latest commit would apply to the older commits. In the end, the question is all about whether or not Apple has the legal ability to sue you for copyright infringement.