I clone repos very often to browse the files in my editor so I didn't like the change initially (and I still don't like it very much) but then after getting used to it I felt that the clone-download section could be positioned above the right side menu which would also allow the menu to be aligned with the box that lists files and dirs.

Anyway, I liked the article even though I am not a UI person

I don't think he means that it's rarely used so much as it's done rarely by the user. When visiting a project page, users likely won't need to clone as often as they'll need to do various other things on a page.

No, you're not atypical. If I want to look into some project closer (and that's why I'm searching or visiting particular github page in the first place, well, more often than not), then I copy git:// URL and download git repo. Real fiddling happens locally later.

GitHub's answer to this is "just copy the URL from your browser." It means using http(s) cloning which may or may not be desired, but from a UX perspective I think that it is neat.