Many filesystems cannot represent empty directories. Many archive formats also do not. I don't think this a problem in practice. I find this argument extremely weak.
Like which ones? And how does mkdir(1) work on such filesystems?
Every mail server since postfix supports Maildir, in which every email is a file in one of 3 subdirectories (tmp, new or cur) of a user directory. If there's no jbloggs/tmp dir, postfix will think user jbloggs does not exist. So if you want to take a restorable snapshot of this with git, there needs to be a file there. I don't know if jbloggs/tmp/README would cause a problem, because I don't know how postfix will treat the presence of a file with a name that violates its expected syntax (which includes a timestamp and other metadata), but what I do know is that, after running `git clone any-repo`, I can safely delete every .gitkeep file to restore the system to its original state without having to understand that repo in detail -- while I cannot safely delete every README file. That's because the commonly understood semantics of .gitkeep is "I exist solely to shoehorn this empty dir into git", which does not apply to other files.
> Many filesystems cannot represent empty directories
Your turn -- name one.