But it's not really surprising that one can't commit empty directories, one can't commit directories at all. Git is a tool for version controlling the lines and bytes of source code under version control. It's a deliberate decision to focus solely on that.
Consider that what is one person's ease of use can be another's pain in the ass. I'm thankful that git has not chosen the path of trying to cater to everyone and their esoteric use cases. I've used other tools that do and it ends up creating a mess instead. Instead it does one thing and it does it well.
I think that if you dig you'll find that if there's something git doesn't do or doesn't do well, that's because a lot of smart people have already looked at that problem and come to the conclusion you shouldn't do things that way.