One good reason for me personally is to insure future availability. As I type this, there are a couple of videos in my watch-later playlist that have been replaced with "video removed".
It also automatically doesn't download things you already have, so it can be used periodically to sync the list if you want.
It only really matters if you expect videos to go down, but I also have my small collection of "videos that were obviously going to be taken down".
I think because of its name people also don't realize that youtube-dl works for LOTS of other sites and it's relatively easy to add new sites in as well.