Well, first of all, purge will not leave __delete_if_empty directories unless the directory is not in fact empty. These files are actually markers for purge so it knows which directories it can delete (once they are empty).
Yeah, I played around with purge just to see how it handled things. It works well. In that, it'll only keep folders there with hand-edited files in them. And, if you do a redeploy, you'll now have a strictly valid installation again.
But, I have noticed that if I /uninstall/ a mod, it'll leave empty folders. So, until a user does do that purge/deploy cycle, they'll potentially have that messy file structure that I've seen a few times. I think most of those times were when I was just getting back into using Vortex and didn't even know what purge was used for. I use purge quite a lot now, just to keep things tidy.