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.

To manually install it, you must clone the repo. Then you have to download models into the right place. Where's the right place? Well, there's an empty directory called models. They go in there.

IMO that's an effective use of gitkeep.