> Truly, what purpose does this serve?

The simplest answer is that sometimes other existing software that I need to use treats an empty directory (or, hopefully, a directory containing just an irrelevant file like .gitkeep) differently from an absent directory, and I want that software to behave in the first way instead of the second.

A more thorough answer would be: Filesystems can represent empty directories, so a technology that supports versioned filesystems should be able to as well. And if that technology can't quite support fully versioned filesystems -- perhaps because it was never designed with that goal in mind -- but can nevertheless support them well enough to cover a huge number of use cases that people actually have, then massaging it a bit to handle those rough edges still makes sense.