How can I discover which files were deleted by `rm -rf`?
There is no way to know for certain exactly which files were deleted. There's no list stored, no trash can, this is unix (well BSD) and you don't get any nice second chances with rm -rf

As you have seen though, you can infer what might have been deleted first by observing the rm command's behaviour.

I created a folder with a few subfolders, including some with a period at the beginning of the name and threw a few files into each.

The order is always alphabetical with the hidden, period prefixed directories getting deleted first.

If you compare a backup with your directory structure, once you have moved through alphabetically and started to find files in the backup that are still on your main drive, I think you can rest assured that you haven't missed any other files.